How to convert an EXE file for Windows CE without Active Sync

Question

I'm able to compile and use Active Sync 4.5 to copy and then run application files in a Windows CE based device. Whenever I copy a file to the device Active Sync will say it will convert the file.

This process of manually uploading the files using Active Sync is slow so I'm now sending the files directly using my application and a TCP sort of file receiver. File is being transferred fine (crc checked).

The problem is that the file does not run complaining with a generic message that the file cannot be opened. My first and only guess is related to this "conversion" process that Active Sync is doing.

I could not find any documentation related to what is is this process and how does it work. Is there any place I can find more information about this conversion? Or is there any tool that can pre-convert so I can transfer it?

The first idea about pre-convert was to copy the file to the device and the copy it back using Active Sync but when copying files out of Windows CE it will convert back to PC format.