Wix Custom BA properly handle upgrade

Question

I've been fighting with the Wix custom bootstrapper for days trying to get the upgrade to work properly. The BA upgrade code remains the same while the MSI files have new product codes. I only display the BA in the ARP, not the MSI. I've gotten it to the point that it properly upgrades all the MSI files, but when it gets to the end and opens the old bundle to uninstall it, it opens and executes, but the entry in the ARP remains so that now I have two.

Here is the full code (minus some GUI specific code):

public class MainViewModel : ViewModelBase
{
    public MainViewModel(BootstrapperApplication bootstrapper)
    {
        isInstall = true;
        isUpgrade = false;
        isOldBundle = false;
        userHasCancelled = false;
        encounteredError = false;
        ExitEnabled = true;
        installedArchitecture = "";

        this.Bootstrapper = bootstrapper;

        //Add listeners to all the events here

        Command command = bootstrapper.Command;
        if (command.Action == LaunchAction.Uninstall) {
            isInstall = false;
            if (command.Display == Display.Embedded) {
                isOldBundle = true;
            }
        }

        if (!isOldBundle) {
            Messenger.Default.Register<SwitchViewMessage>(this, (switchViewMessage) =>
            {
                SwitchView(switchViewMessage.ViewName);
            });

            SwitchView("Install");
        }
    }

    private bool install64Bit()
    {
        return optionsDataContext.SelectedArchitecture == 0;
    }

    private bool isInstall;
    private bool isUpgrade;
    private bool userHasCancelled;
    private bool encounteredError;

    public BootstrapperApplication Bootstrapper { get; private set; }

    private void OptionsExecute()
    {
        SwitchView("Options");
    }

    private void InstallExecute()
    {
        if (FrameView == optionsView) {
            //Ok pressed in Options View
            optionsDataContext.StoreLastInstallLocation();
            SwitchView("Install");
        } else if (installDataContext.AcceptLicense) {                
            Bootstrapper.Engine.StringVariables["InstallFolder"] = optionsDataContext.InstallLocation;

            Bootstrapper.Engine.Plan(LaunchAction.Install);
            SwitchView("Progress");
        } else {
            TopMostMessageBox.Show("You must accept the License Agreement.", "Error");
        }
    }

    private void UninstallExecute()
    {
        Bootstrapper.Engine.Plan(LaunchAction.Uninstall);
        SwitchView("Progress");
    }

    private void ExitExecute()
    {
        if (FrameView == optionsView) {
            //Cancel pressed in Options View
            optionsDataContext.RestoreLastInstallLocation();
            SwitchView("Install");
        } else if (FrameView == progressView) {
            //Cancel mid installation
            userHasCancelled = true;
            this.ExitEnabled = false;
            SwitchView("Complete");
        } else {
            if (FrameView == completeView) {
                if (!userHasCancelled && !encounteredError && isInstall && completeDataContext.LaunchApplication) {
                    string exePath = optionsDataContext.InstallLocation + "\\program\\flexsim.exe";
                    ProcessStartInfo exeFile = new ProcessStartInfo(exePath);
                    Process.Start(exeFile);
                }
            }
            FlexSimBootstrapper.BootstrapperDispatcher.InvokeShutdown();
        }
    }

    private void OnApplyComplete(object sender, ApplyCompleteEventArgs e)
    {
        OptionsEnabled = false;
        InstallEnabled = false;
        UninstallEnabled = false;
        if (e.Status < 0) {
            userHasCancelled = true;
            SwitchView("Complete");
        }
    }

    private string installedArchitecture;

    private void OnDetectPackageComplete(object sender, DetectPackageCompleteEventArgs e)
    {
        if (isOldBundle) { //Don't do anything with packages, we're just uninstalling the bundle
            return;
        }
        if (e.PackageId.StartsWith("FlexSim")) {
            if (!isInstall) {
                //If we're being upgraded, the packages were already upgraded

            } else {
                if (e.State == PackageState.Absent) {
                    if (installedArchitecture.Length > 0)
                        return;
                    OptionsEnabled = true;
                    isInstall = true;
                    this.InstallEnabled = true; //Update the InstallView
                } else if (e.State == PackageState.Present) {
                    installedArchitecture = e.PackageId.Substring(e.PackageId.Length - 3, 3);
                    isInstall = false;
                    this.InstallEnabled = false; //Update the InstallView
                    UninstallEnabled = true;
                }
            }
        } else {
            string architecture = (install64Bit() ? "x64" : "x86");
            if (installedArchitecture.Length > 0)
                architecture = installedArchitecture;

            if (isInstall) {
                //If this is a bug fix release, check to see which modules are already installed and
                //whether there are modules to be updated
                if (e.PackageId == ("Conveyor_" + architecture)) {
                    if (e.State == PackageState.Present) {
                        installDataContext.ConveyorEnabled = false;
                    } else {
                        installDataContext.InstallConveyor = true;
                    }
                } else if (e.PackageId == ("AGV_" + architecture)) {
                    if (e.State == PackageState.Present) {
                        installDataContext.AGVEnabled = false;
                    } else {
                        installDataContext.InstallAGV = true;
                    }
                } else if (e.PackageId == ("AStar_" + architecture)) {
                    if (e.State == PackageState.Present) {
                        installDataContext.AStarEnabled = false;
                    } else {
                        installDataContext.InstallAStar = true;
                    }
                }
            } else {
                  //Check to see which modules were installed and only show those checkboxes
                if (e.PackageId == ("Conveyor_" + architecture)) {
                    if (e.State == PackageState.Absent) {
                        installDataContext.ConveyorEnabled = false;
                    } else {
                        installDataContext.InstallConveyor = true;
                    }
                } else if (e.PackageId == ("AGV_" + architecture)) {
                    if (e.State == PackageState.Absent) {
                        installDataContext.AGVEnabled = false;
                    } else {
                        installDataContext.InstallAGV = true;
                    }
                } else if (e.PackageId == ("AStar_" + architecture)) {
                    if (e.State == PackageState.Absent) {
                        installDataContext.AStarEnabled = false;
                    } else {
                        installDataContext.InstallAStar = true;
                    }
                }
            }
        }
    }

    private void OnPlanPackageBegin(object sender, PlanPackageBeginEventArgs e)
    {
        if (isOldBundle) { //Don't do anything with packages, we're just uninstalling the bundle
            return;
        }
        string architecture = install64Bit() ? "x64" : "x86";
        if (e.PackageId.StartsWith("Conveyor")) {
            bool installConveyor = installDataContext.InstallConveyor && installDataContext.ConveyorEnabled && e.PackageId.EndsWith(architecture);
            e.State = installConveyor ? (isInstall ? RequestState.Present : RequestState.Absent) : RequestState.None;
        } else if (e.PackageId.StartsWith("AGV")) {
            bool installAGV = installDataContext.InstallAGV && installDataContext.AGVEnabled && e.PackageId.EndsWith(architecture);
            e.State = installAGV ? (isInstall ? RequestState.Present : RequestState.Absent) : RequestState.None;
        } else if (e.PackageId.StartsWith("AStar")) {
            bool installAStar = installDataContext.InstallAStar && installDataContext.AStarEnabled && e.PackageId.EndsWith(architecture);
            e.State = installAStar ? (isInstall ? RequestState.Present : RequestState.Absent) : RequestState.None;
        } else if (e.PackageId.StartsWith("FlexSim")) {
            e.State = e.PackageId.EndsWith(architecture) ? (isInstall ? RequestState.Present : RequestState.Absent) : RequestState.None;
        }
    }

    private void OnPlanComplete(object sender, PlanCompleteEventArgs e)
    {
        if (e.Status >= 0)
            Bootstrapper.Engine.Apply(System.IntPtr.Zero);
    }

    private void OnExecuteMsiMessage(object sender, ExecuteMsiMessageEventArgs e)
    {
        if (e.MessageType == InstallMessage.ActionStart) {
            string text = e.Message.Split(' ')[2];
            text = text.TrimEnd('.');

            //Turn the camel case text into a more readable format
            var r = new Regex(@"
             (?<=[A-Z])(?=[A-Z][a-z]) |
             (?<=[^A-Z])(?=[A-Z]) |
             (?<=[A-Za-z])(?=[^A-Za-z])", RegexOptions.IgnorePatternWhitespace);

            progressDataContext.ProgressText = r.Replace(text, " ");
        }
    }

    private void OnProgress(object sender, ProgressEventArgs e)
    {
        progressDataContext.ProgressPercent = e.OverallPercentage;

        // handle user cancellations here
        if (userHasCancelled)
            e.Result = Result.Cancel;
    }

    private void OnExecuteProgress(object sender, ExecuteProgressEventArgs e)
    {
        progressDataContext.ProgressPercent = e.ProgressPercentage;

        if (userHasCancelled)
            e.Result = Result.Cancel;
    }

    private void OnCacheAcquireProgress(object sender, CacheAcquireProgressEventArgs e)
    {
        progressDataContext.ProgressPercent = e.OverallPercentage;
        string packageName = e.PackageOrContainerId.Substring(0, e.PackageOrContainerId.Length - 4); //Remove architecture
        progressDataContext.ProgressText = "Downloading " + packageName + (packageName == "FlexSim" ? "" : "Module");

        if (userHasCancelled)
            e.Result = Result.Cancel;
    }

    private void OnCacheAcquireBegin(object sender, CacheAcquireBeginEventArgs e)
    {
        progressDataContext.ProgressPercent = 0;
        string packageName = e.PackageOrContainerId.Substring(0, e.PackageOrContainerId.Length - 4); //Remove architecture
        progressDataContext.ProgressText = "Beginning download of " + packageName + (packageName == "FlexSim" ? "" : "Module");
    }

    private void OnCacheAcquireComplete(object sender, CacheAcquireCompleteEventArgs e)
    {
        progressDataContext.ProgressPercent = 100; 
        string packageName = e.PackageOrContainerId.Substring(0, e.PackageOrContainerId.Length - 4); //Remove architecture
        progressDataContext.ProgressText = "Download of " + packageName + (packageName == "FlexSim" ? "" : "Module") + " Complete";
    }

    private void OnCacheComplete(object sender, CacheCompleteEventArgs e)
    {
        progressDataContext.ProgressPercent = 100;
        progressDataContext.PackageName = "Download Complete";
        progressDataContext.ProgressText = "";
    }

    private void OnError(object sender, ErrorEventArgs e)
    {
        string packageName = e.PackageId.Substring(0, e.PackageId.Length - 4); //Remove architecture
        if (e.PackageId == "Netfx4Full")
            packageName = ".NET 4.0";
        TopMostMessageBox.Show(e.ErrorMessage, "Error " + (isUpgrade ? "Upgrading" : (isInstall ? "Installing" : "Uninstalling")) + " " + packageName);
        if (packageName == "FlexSim" || packageName == ".NET 4.0")
            encounteredError = true; //Rollback
    }

    private void OnExecuteFilesInUse(object sender, ExecuteFilesInUseEventArgs e)
    {
        string packageName = e.PackageId.Substring(0, e.PackageId.Length - 4); //Remove architecture
        if (e.PackageId == "Netfx4Full")
            packageName = ".NET 4.0";
        DialogResult result = TopMostMessageBox.Show("Unable to continue installation, files are in use. Please close FlexSim before continuing.", "Error " + (isInstall ? "Installing" : "Uninstalling") + " " + packageName, MessageBoxButtons.RetryCancel);
        if (result == DialogResult.Cancel)
            encounteredError = true; //Rollback
    }

    private void OnExecutePackageBegin(object sender, ExecutePackageBeginEventArgs e)
    {
        progressDataContext.ProgressPercent = 0;
        string packageName = e.PackageId.Substring(0, e.PackageId.Length - 4); //Remove architecture
        Guid relatedBundle;
        if (Guid.TryParse(e.PackageId.Substring(1, e.PackageId.Length - 2), out relatedBundle)) {
            progressDataContext.PackageName = "Cleaning Up...";
            progressDataContext.ProgressText = "";
        } else {
            progressDataContext.PackageName = (isUpgrade ? "Upgrading" : (isInstall ? "Installing" : "Uninstalling")) + " " + packageName + "...";
            progressDataContext.ProgressText = "Opening package";
        }
    }

    private void OnExecutePackageComplete(object sender, ExecutePackageCompleteEventArgs e)
    {
        progressDataContext.ProgressPercent = 100;
    }

   private void OnExecuteComplete(object sender, ExecuteCompleteEventArgs e)
    {
        if (isUpgrade && !isInstall) {
            //Uninstalling the old bootstrapper
            Bootstrapper.Engine.Quit(0);
            Environment.Exit(0);
            return;
        }

        SwitchView("Complete");
    }

   private void OnResolveSource(object sender, ResolveSourceEventArgs e)
   {
       string architecture = install64Bit() ? "x64" : "x86";
       if (!string.IsNullOrEmpty(e.DownloadSource) && e.PackageOrContainerId.EndsWith(architecture))
       {
           e.Result = Result.Download;

           progressDataContext.PackageName = "Please wait, downloading installation files...";
           progressDataContext.ProgressText = "Contacting server";
       }
   }

   private void OnDetectRelatedBundle(object sender, DetectRelatedBundleEventArgs e)
   {
       if (e.Version.ToString() == "7.5.0.0") {
           TopMostMessageBox.Show("Please uninstall FlexSim 7.5.0 before running this installer.", "Error");
           Environment.Exit(0);
       } else {
           isUpgrade = true;
           if (Bootstrapper.Command.Display == Display.Embedded) {
               //This bootstrapper is being run after FlexSim was upgraded in order to remove it from the ARP
               Bootstrapper.Engine.Plan(LaunchAction.Uninstall);
           } else {
               installDataContext.IsUpgrade = true;
               this.AppName = getFullProductName() + " Upgrade";
               this.InstallName = "Upgrade";
           }
       }
   }

Here's the log from the upgrading bundle:

Burn v3.9.1006.0, Windows v6.2 (Build 9200: Service Pack 0), path: \\hulk\Temp\Matt Long\FlexSim7.5.4\FlexSimInstaller.exe, cmdline: ''
Setting string variable 'WixBundleLog' to value 'C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.4_20150303100732.log'
Setting string variable 'WixBundleOriginalSource' to value '\\hulk\Temp\Matt Long\FlexSim7.5.4\FlexSimInstaller.exe'
Setting string variable 'WixBundleOriginalSourceFolder' to value '\\hulk\Temp\Matt Long\FlexSim7.5.4\'
Setting string variable 'WixBundleName' to value 'FlexSim 7.5.4'
Loading managed bootstrapper application.
Creating BA thread to run asynchronously.
Launching FlexSimBootstrapper UX
Detect begin, 9 packages
Setting string variable 'Netfx4x64FullVersion' to value '4.5.50709'
Setting string variable 'Netfx4FullVersion' to value '4.5.50709'
Detected related bundle: {c2bb38d9-e545-4dee-a6e6-2e483f088a7a}, type: Upgrade, scope: PerMachine, version: 7.5.2.0, operation: MajorUpgrade
Condition 'Netfx4FullVersion AND (NOT VersionNT64 OR Netfx4x64FullVersion)' evaluates to true.
Detected related package: {65565599-386F-4A2A-B63E-88A873AE8AB8}, scope: PerMachine, version: 7.5.2.0, language: 0 operation: MajorUpgrade
Detected related package: {65565599-386F-4A2A-B63E-88A873AE8AB8}, scope: PerMachine, version: 7.5.2.0, language: 0 operation: MajorUpgrade
Detected related package: {65565599-386F-4A2A-B63E-88A873AE8AB8}, scope: PerMachine, version: 7.5.2.0, language: 0 operation: MajorUpgrade
Detected related package: {65565599-386F-4A2A-B63E-88A873AE8AB8}, scope: PerMachine, version: 7.5.2.0, language: 0 operation: MajorUpgrade
Detected package: Netfx4Full, state: Present, cached: None
Detected package: FlexSim_x86, state: Absent, cached: None
Detected package: FlexSim_x64, state: Absent, cached: None
Detected package: Conveyor_x86, state: Absent, cached: None
Detected package: AGV_x86, state: Absent, cached: None
Detected package: AStar_x86, state: Absent, cached: None
Detected package: Conveyor_x64, state: Absent, cached: None
Detected package: AGV_x64, state: Absent, cached: None
Detected package: AStar_x64, state: Absent, cached: None
Detect complete, result: 0x0
Setting string variable 'InstallFolder' to value 'C:\Program Files\FlexSim7.5'
Plan begin, 9 packages, action: Install
Condition '(VersionNT < v6.0 OR VersionNT64 < v6.0) AND (NOT (Net4FullVersion OR Net4x64FullVersion))' evaluates to false.
Skipping dependency registration on package with no dependency providers: Netfx4Full
Setting string variable 'WixBundleRollbackLog_FlexSim_x64' to value 'C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.4_20150303100732_0_FlexSim_x64_rollback.log'
Setting string variable 'WixBundleLog_FlexSim_x64' to value 'C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.4_20150303100732_0_FlexSim_x64.log'
Condition 'NOT Installed' evaluates to true.
Condition 'NOT Installed' evaluates to true.
Condition 'NOT Installed' evaluates to true.
Condition 'NOT Installed' evaluates to true.
Condition 'NOT Installed' evaluates to true.
Condition 'NOT Installed' evaluates to true.
Planned package: Netfx4Full, state: Present, default requested: Absent, ba requested: Absent, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: FlexSim_x86, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: FlexSim_x64, state: Absent, default requested: Present, ba requested: Present, execute: Install, rollback: Uninstall, cache: Yes, uncache: No, dependency: Register
Planned package: Conveyor_x86, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: AGV_x86, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: AStar_x86, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: Conveyor_x64, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: AGV_x64, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned package: AStar_x64, state: Absent, default requested: Present, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Planned related bundle: {c2bb38d9-e545-4dee-a6e6-2e483f088a7a}, type: Upgrade, default requested: Absent, ba requested: Absent, execute: Uninstall, rollback: Install, dependency: None
Plan complete, result: 0x0
Apply begin
Creating a system restore point.
Created a system restore point.
Caching bundle from: 'C:\Users\DEVELO~1\AppData\Local\Temp\{67225db2-d963-4067-ba1b-f42a8f1f6dcb}\.be\FlexSimInstaller.exe' to: 'C:\ProgramData\Package Cache\{67225db2-d963-4067-ba1b-f42a8f1f6dcb}\FlexSimInstaller.exe'
Registering bundle dependency provider: {67225db2-d963-4067-ba1b-f42a8f1f6dcb}, version: 7.5.4.0
Acquiring package: FlexSim_x64, payload: FlexSim_x64, copy from: \\hulk\Temp\Matt Long\FlexSim7.5.4\flexsim__7.5.4._x64
Setting string variable 'WixBundleLastUsedSource' to value '\\hulk\Temp\Matt Long\FlexSim7.5.4\'
Verified acquired payload: FlexSim_x64 at path: C:\ProgramData\Package Cache\.unverified\FlexSim_x64, moving to: C:\ProgramData\Package Cache\{DE2D8A1C-DD4A-411C-A23B-A9C0943AFC84}v7.5.4\flexsim__7.5.4._x64.
Registering package dependency provider: {DE2D8A1C-DD4A-411C-A23B-A9C0943AFC84}, version: 7.5.4, package: FlexSim_x64
Applying execute package: FlexSim_x64, action: Install, path: C:\ProgramData\Package Cache\{DE2D8A1C-DD4A-411C-A23B-A9C0943AFC84}v7.5.4\flexsim__7.5.4._x64, arguments: ' ARPSYSTEMCOMPONENT="1" MSIFASTINSTALL="7" INSTALLDIR="C:\Program Files\FlexSim7.5"'
Applied execute package: FlexSim_x64, result: 0x0, restart: None
Registering dependency: {67225db2-d963-4067-ba1b-f42a8f1f6dcb} on package provider: {DE2D8A1C-DD4A-411C-A23B-A9C0943AFC84}, package: FlexSim_x64
Applying execute package: {c2bb38d9-e545-4dee-a6e6-2e483f088a7a}, action: Uninstall, path: C:\ProgramData\Package Cache\{c2bb38d9-e545-4dee-a6e6-2e483f088a7a}\FlexSimInstaller.exe, arguments: '"C:\ProgramData\Package Cache\{c2bb38d9-e545-4dee-a6e6-2e483f088a7a}\FlexSimInstaller.exe" -uninstall -quiet -burn.related.upgrade -burn.ancestors={67225db2-d963-4067-ba1b-f42a8f1f6dcb}'
Applied execute package: {c2bb38d9-e545-4dee-a6e6-2e483f088a7a}, result: 0x0, restart: None
Apply complete, result: 0x0, restart: None, ba requested restart:  No
Shutting down, exit code: 0x0
Variable: InstallFolder = C:\Program Files\FlexSim7.5
Netfx4FullVersion = 4.5.50709
Netfx4x64FullVersion = 4.5.50709
VersionNT = 6.2.0.0
VersionNT64 = 6.2.0.0
Variable:WixBundleAction = 4
Variable: WixBundleElevated = 1
Variable: WixBundleLastUsedSource = \\hulk\Temp\Matt Long\FlexSim7.5.4\
Variable: WixBundleLog = C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.4_20150303100732.log
Variable: WixBundleLog_FlexSim_x64 = C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.4_20150303100732_0_FlexSim_x64.log
Variable: WixBundleManufacturer = FlexSim Software Products, Inc.
Variable: WixBundleName = FlexSim 7.5.4
Variable: WixBundleOriginalSource = \\hulk\Temp\Matt Long\FlexSim7.5.4\FlexSimInstaller.exe
Variable: WixBundleOriginalSourceFolder = \\hulk\Temp\Matt Long\FlexSim7.5.4\
Variable: WixBundleProviderKey = {67225db2-d963-4067-ba1b-f42a8f1f6dcb}
Variable: WixBundleRollbackLog_FlexSim_x64 = C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.4_20150303100732_0_FlexSim_x64_rollback.log
Variable: WixBundleTag = FlexSim
Variable: WixBundleVersion = 7.5.4.0
Exit code: 0x0, restarting: No

And for uninstalling the old bundle:

Burn v3.9.1006.0, Windows v6.2 (Build 9200: Service Pack 0), path: C:\ProgramData\Package Cache\{c2bb38d9-e545-4dee-a6e6-2e483f088a7a}\FlexSimInstaller.exe, cmdline: '-burn.unelevated BurnPipe.{75719B82-36F8-4EEC-9627-95F9C80EFD3D} {C5DDF0F8-2C71-4784-918C-123444FEB511} 3048 -uninstall -quiet -burn.related.upgrade -burn.ancestors={67225db2-d963-4067-ba1b-f42a8f1f6dcb} -burn.embedded BurnPipe.{FD72859F-485B-49ED-955A-3BE174642F7C} {7C01F82A-C3C3-42F9-AF31-0E9995FB9E61} 4480'
This bundle is being run by a related bundle as type 'Upgrade'.
Setting string variable 'WixBundleLog' to value 'C:\Users\DEVELO~1\AppData\Local\Temp\FlexSim_7.5.2_20150303100853.log'
Loading managed bootstrapper application.
Creating BA thread to run asynchronously.
Launching FlexSimBootstrapper UX
Detect begin, 9 packages
Setting string variable 'Netfx4x64FullVersion' to value '4.5.50709'
Setting string variable 'Netfx4FullVersion' to value '4.5.50709'
Detected related bundle: {67225db2-d963-4067-ba1b-f42a8f1f6dcb}, type: Upgrade, scope: PerMachine, version: 7.5.4.0, operation: None
Condition 'Netfx4FullVersion AND (NOT VersionNT64 OR Netfx4x64FullVersion)' evaluates to true.
Detected partially cached package: FlexSim_x86, invalid payload: FlexSim_x86, reason: 0x80070002
Detected related package: {DE2D8A1C-DD4A-411C-A23B-A9C0943AFC84}, scope: PerMachine, version: 7.5.4.0, language: 0 operation: Downgrade
Detected related package: {DE2D8A1C-DD4A-411C-A23B-A9C0943AFC84}, scope: PerMachine, version: 7.5.4.0, language: 0 operation: Downgrade
Detected package: Netfx4Full, state: Present, cached: None
Detected package: FlexSim_x86, state: Obsolete, cached: Partial
Detected package: FlexSim_x64, state: Obsolete, cached: Complete
Detected package: Conveyor_x86, state: Absent, cached: None
Detected package: AGV_x86, state: Absent, cached: None
Detected package: AStar_x86, state: Absent, cached: None
Detected package: Conveyor_x64, state: Absent, cached: None
Detected package: AGV_x64, state: Absent, cached: None
Detected package: AStar_x64, state: Absent, cached: None
Detect complete, result: 0x0
Plan begin, 9 packages, action: Uninstall
Plan skipped related bundle: {67225db2-d963-4067-ba1b-f42a8f1f6dcb}, type: Upgrade, because it was previously scheduled.
Skipping dependency registration on package with no dependency providers: Netfx4Full
Planned related bundle: {67225db2-d963-4067-ba1b-f42a8f1f6dcb}, type: Upgrade, default requested: None, ba requested: None, execute: None, rollback: None, dependency: None
Planned package: AStar_x64, state: Absent, default requested: Absent, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: Unregister
Planned package: AGV_x64, state: Absent, default requested: Absent, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: Unregister
Planned package: Conveyor_x64, state: Absent, default requested: Absent, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: Unregister
Planned package: AStar_x86, state: Absent, default requested: Absent, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: Unregister
Planned package: AGV_x86, state: Absent, default requested: Absent, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: Unregister
Planned package: Conveyor_x86, state: Absent, default requested: Absent, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: Unregister
Planned package: FlexSim_x64, state: Obsolete, default requested: None, ba requested: Absent, execute: None, rollback: None, cache: No, uncache: Yes, dependency: Unregister
Planned package: FlexSim_x86, state: Obsolete, default requested: None, ba requested: None, execute: None, rollback: None, cache: No, uncache: Yes, dependency: Unregister
Planned package: Netfx4Full, state: Present, default requested: None, ba requested: None, execute: None, rollback: None, cache: No, uncache: No, dependency: None
Plan complete, result: 0x0
Apply begin
Removed package dependency provider: {124DDD12-0BD0-464E-B753-4BC53D27770A}, package: AStar_x64
Removed package dependency provider: {E48B3FBD-001F-4D1F-876B-B041044B6B87}, package: AGV_x64
Removed package dependency provider: {65E44AB7-FBC5-480A-92B5-519CF57F6CDD}, package: Conveyor_x64
Removed package dependency provider: {124DDD12-0BD0-464E-B753-4BC53D27770A}, package: AStar_x86
Removed package dependency provider: {E48B3FBD-001F-4D1F-876B-B041044B6B87}, package: AGV_x86
Removed package dependency provider: {65E44AB7-FBC5-480A-92B5-519CF57F6CDD}, package: Conveyor_x86
Removed dependency: {c2bb38d9-e545-4dee-a6e6-2e483f088a7a} on package provider: {65565599-386F-4A2A-B63E-88A873AE8AB8}, package FlexSim_x64

Answer 1

I had a similar problem where our previous product installer is an Msi and now we have a first version of a Managed Bootstrapper Application where several pre requisites and the MSI are bundled. We had to upgrade the currently installed product. All I did was set MsiProperty UPGRADE=1 for the relevant Msi package in the chain in the Bundle.wxs.

Look at my answer at Upgrade older msi from Wix custom BA Bundle

Answer 2

I finally figured it out! As suspected it was something small. It was all about timing.

The first issue was that I needed to perform the plan uninstall in the DetectComplete action:

   private void OnDetectComplete(object sender, DetectCompleteEventArgs e)
   {
       if (Bootstrapper.Command.Action == LaunchAction.Uninstall && Bootstrapper.Command.Display == Display.Embedded)
       {
           Bootstrapper.Engine.Plan(LaunchAction.Uninstall);
       }
   }

Then the reason the log from the uninstalling of the old bundle was cut short was due to my exiting of the application prematurely. I moved that to the ApplyComplete action:

    private void OnApplyComplete(object sender, ApplyCompleteEventArgs e)
    {
        if (Bootstrapper.Command.Action == LaunchAction.Uninstall && Bootstrapper.Command.Display == Display.Embedded) {
            //Uninstalling the old bootstrapper
            Bootstrapper.Engine.Quit(0);
            Environment.Exit(0);
        }
    }

Answer 3

Burn is too complex to be able to diagnose off of only stripped down code. We would need the real code and/or the Burn logs from both the old bundle that is getting uninstalled and the new bundle that is getting installed.

You should usually use the LaunchAction from the Command.Action property to decide which action to take. If you do that, increment the version of your bundle, and remove your On*RelatedBundle methods, it should work. Your OnPlanPackageBegin method should probably also be removed, Burn will install packages during the Install action and remove packages during the Uninstall action by default. Also, don't bother setting e.Result to Result.Error, it won't do anything.