A single folder mysteriously not downloaded from or compressed on ftp server

Question

So I've done a lot of research so far and haven't found even a hint of something that could cause this. I put htaccess in the tags since I thought that could technically do it.

The problem is this: I have a server to migrate. So I want to download all the files from the old server, and then reupload to the new server. What happens when I go to the online file manager and click compress and download is that a very important folder is missing from the zip (and judging by the counts there are others missing too).

I've also used Filezilla to recursively download the whole directory structure, but it also misses that folder. Even stranger is that Filezilla sees the folder and I can download it directly, but if I recursively download the folder just above it, it doesn't grab it. It's the same with the online file manager, it sees it too.

I even wrote my own c# program to do a basic directory listing and it doesn't see it. It uses an FtpWebRequest with Method set to WebRequestMethods.Ftp.ListDirectoryDetails.

So the problems persists on both server side functions as well as the client attempts through FTP protocols.

There is an .htaccess file specific to the folder in question but I can't see anything that might do this. (Included below)

Does anyone have any ideas? I'd be most grateful for any hint

<IfModule mod_headers.c>
  <FilesMatch "\.(js|css|xml|gz|svgz)$">
    Header append Vary Accept-Encoding
  </FilesMatch>
</IfModule>

  <FilesMatch "\.(htm|php|js|css|htc|png|gif|jpe?g|ico|xml|csv|txt|swf|flv|eot|woff|svg|svgz|ttf|pdf|gz)$">
    RewriteEngine Off
  </FilesMatch>

  # Apache configuration file
# httpd.apache.org/docs/2.2/mod/quickreference.html

# Note .htaccess files are an overhead, this logic should be in your Apache
# config if possible: httpd.apache.org/docs/2.2/howto/htaccess.html

# Techniques in here adapted from all over, including:
# Kroc Camen: camendesign.com/.htaccess
# perishablepress.com/press/2006/01/10/stupid-htaccess-tricks/
# Sample .htaccess file of CMS MODx: modxcms.com


# ----------------------------------------------------------------------
# Better website experience for IE users
# ----------------------------------------------------------------------

# Force the latest IE version, in various cases when it may fall back to IE7 mode
# github.com/rails/rails/commit/123eb25#commitcomment-118920
# Use ChromeFrame if it's installed for a better experience for the poor IE folk

<IfModule mod_headers.c>
  Header set X-UA-Compatible "IE=Edge,chrome=1"
  # mod_headers can't match by content-type, but we don't want to send this header on *everything*...
  <FilesMatch "\.(js|css|gif|png|jpe?g|pdf|xml|oga|ogg|m4a|ogv|mp4|m4v|webm|svg|svgz|eot|ttf|otf|woff|ico|webp|appcache|manifest|htc|crx|oex|xpi|safariextz|vcf)$" >
    Header unset X-UA-Compatible
  </FilesMatch>
</IfModule>


# ----------------------------------------------------------------------
# Cross-domain AJAX requests
# ----------------------------------------------------------------------

# Serve cross-domain Ajax requests, disabled by default.
# enable-cors.org
# code.google.com/p/html5security/wiki/CrossOriginRequestSecurity

# <IfModule mod_headers.c>
# Header set Access-Control-Allow-Origin "*"
# </IfModule>


# ----------------------------------------------------------------------
# CORS-enabled images (@crossorigin)
# ----------------------------------------------------------------------

# Send CORS headers if browsers request them; enabled by default for images.
# developer.mozilla.org/en/CORS_Enabled_Image
# blog.chromium.org/2011/07/using-cross-domain-images-in-webgl-and.html
# hacks.mozilla.org/2011/11/using-cors-to-load-webgl-textures-from-cross-domain-images/
# wiki.mozilla.org/Security/Reviews/crossoriginAttribute

<IfModule mod_setenvif.c>
  <IfModule mod_headers.c>
    # mod_headers, y u no match by Content-Type?!
    <FilesMatch "\.(gif|png|jpe?g|svg|svgz|ico|webp)$">
      SetEnvIf Origin ":" IS_CORS
      Header set Access-Control-Allow-Origin "*" env=IS_CORS
    </FilesMatch>
  </IfModule>
</IfModule>


# ----------------------------------------------------------------------
# Webfont access
# ----------------------------------------------------------------------

# Allow access from all domains for webfonts.
# Alternatively you could only whitelist your
# subdomains like "subdomain.example.com".

<IfModule mod_headers.c>
  <FilesMatch "\.(ttf|ttc|otf|eot|woff|font.css)$">
    Header set Access-Control-Allow-Origin "*"
  </FilesMatch>
</IfModule>


# ----------------------------------------------------------------------
# Proper MIME type for all files
# ----------------------------------------------------------------------

# JavaScript
# Normalize to standard type (it's sniffed in IE anyways)
# tools.ietf.org/html/rfc4329#section-7.2
AddType application/javascript js jsonp
AddType application/json json

# Audio
AddType audio/ogg oga ogg
AddType audio/mp4 m4a f4a f4b

# Video
AddType video/ogg ogv
AddType video/mp4 mp4 m4v f4v f4p
AddType video/webm webm
AddType video/x-flv flv

# SVG
# Required for svg webfonts on iPad
# twitter.com/FontSquirrel/status/14855840545
AddType image/svg+xml svg svgz
AddEncoding gzip svgz

# Webfonts
AddType application/vnd.ms-fontobject eot
AddType application/x-font-ttf ttf ttc
AddType font/opentype otf
AddType application/x-font-woff woff

# Assorted types
AddType image/x-icon ico
AddType image/webp webp
AddType text/cache-manifest appcache manifest
AddType text/x-component htc
AddType application/xml rss atom xml rdf
AddType application/x-chrome-extension crx
AddType application/x-opera-extension oex
AddType application/x-xpinstall xpi
AddType application/octet-stream safariextz
AddType application/x-web-app-manifest+json webapp
AddType text/x-vcard vcf
AddType application/x-shockwave-flash swf
AddType text/vtt vtt


# ----------------------------------------------------------------------
# Allow concatenation from within specific js and css files
# ----------------------------------------------------------------------

# e.g. Inside of script.combined.js you could have
# <!--#include file="libs/jquery-1.5.0.min.js" -->
# <!--#include file="plugins/jquery.idletimer.js" -->
# and they would be included into this single file.

# This is not in use in the boilerplate as it stands. You may
# choose to use this technique if you do not have a build process.

#<FilesMatch "\.combined\.js$">
# Options +Includes
# AddOutputFilterByType INCLUDES application/javascript application/json
# SetOutputFilter INCLUDES
#</FilesMatch>

#<FilesMatch "\.combined\.css$">
# Options +Includes
# AddOutputFilterByType INCLUDES text/css
# SetOutputFilter INCLUDES
#</FilesMatch>


# ----------------------------------------------------------------------
# Gzip compression
# ----------------------------------------------------------------------

<IfModule mod_deflate.c>

  # Force deflate for mangled headers developer.yahoo.com/blogs/ydn/posts/2010/12/pushing-beyond-gzipping/
  <IfModule mod_setenvif.c>
    <IfModule mod_headers.c>
      SetEnvIfNoCase ^(Accept-EncodXng|X-cept-Encoding|X{15}|~{15}|-{15})$ ^((gzip|deflate)\s*,?\s*)+|[X~-]{4,13}$ HAVE_Accept-Encoding
      RequestHeader append Accept-Encoding "gzip,deflate" env=HAVE_Accept-Encoding
    </IfModule>
  </IfModule>

  # HTML, TXT, CSS, JavaScript, JSON, XML, HTC:
  <IfModule filter_module>
    FilterDeclare COMPRESS
    FilterProvider COMPRESS DEFLATE resp=Content-Type $text/html
    FilterProvider COMPRESS DEFLATE resp=Content-Type $text/css
    FilterProvider COMPRESS DEFLATE resp=Content-Type $text/plain
    FilterProvider COMPRESS DEFLATE resp=Content-Type $text/xml
    FilterProvider COMPRESS DEFLATE resp=Content-Type $text/x-component
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/javascript
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/json
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/xml
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/xhtml+xml
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/rss+xml
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/atom+xml
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/vnd.ms-fontobject
    FilterProvider COMPRESS DEFLATE resp=Content-Type $image/svg+xml
    FilterProvider COMPRESS DEFLATE resp=Content-Type $image/x-icon
    FilterProvider COMPRESS DEFLATE resp=Content-Type $application/x-font-ttf
    FilterProvider COMPRESS DEFLATE resp=Content-Type $font/opentype
    FilterChain COMPRESS
    FilterProtocol COMPRESS DEFLATE change=yes;byteranges=no
  </IfModule>

  <IfModule !mod_filter.c>
    # Legacy versions of Apache
    AddOutputFilterByType DEFLATE text/html text/plain text/css application/json
    AddOutputFilterByType DEFLATE application/javascript
    AddOutputFilterByType DEFLATE text/xml application/xml text/x-component
    AddOutputFilterByType DEFLATE application/xhtml+xml application/rss+xml application/atom+xml
    AddOutputFilterByType DEFLATE image/x-icon image/svg+xml application/vnd.ms-fontobject application/x-font-ttf font/opentype
  </IfModule>

</IfModule>


# ----------------------------------------------------------------------
# Expires headers (for better cache control)
# ----------------------------------------------------------------------

# These are pretty far-future expires headers.
# They assume you control versioning with filename-based cache busting
# Additionally, consider that outdated proxies may miscache
# www.stevesouders.com/blog/2008/08/23/revving-filenames-dont-use-querystring/

# If you don't use filenames to version, lower the CSS and JS to something like
# "access plus 1 week".

<IfModule mod_expires.c>
  ExpiresActive on

# Perhaps better to whitelist expires rules? Perhaps.
  ExpiresDefault "access plus 1 month"

# cache.appcache needs re-requests in FF 3.6 (thanks Remy ~Introducing HTML5)
  ExpiresByType text/cache-manifest "access plus 0 seconds"

# Your document html
  ExpiresByType text/html "access plus 0 seconds"

# Data
  ExpiresByType text/xml "access plus 0 seconds"
  ExpiresByType application/xml "access plus 0 seconds"
  ExpiresByType application/json "access plus 0 seconds"

# Feed
  ExpiresByType application/rss+xml "access plus 1 hour"
  ExpiresByType application/atom+xml "access plus 1 hour"

# Favicon (cannot be renamed)
  ExpiresByType image/x-icon "access plus 1 week"

# Media: images, video, audio
  ExpiresByType image/gif "access plus 1 month"
  ExpiresByType image/png "access plus 1 month"
  ExpiresByType image/jpeg "access plus 1 month"
  ExpiresByType video/ogg "access plus 1 month"
  ExpiresByType audio/ogg "access plus 1 month"
  ExpiresByType video/mp4 "access plus 1 month"
  ExpiresByType video/webm "access plus 1 month"

# HTC files (css3pie)
  ExpiresByType text/x-component "access plus 1 month"

# Webfonts
  ExpiresByType application/x-font-ttf "access plus 1 month"
  ExpiresByType font/opentype "access plus 1 month"
  ExpiresByType application/x-font-woff "access plus 1 month"
  ExpiresByType image/svg+xml "access plus 1 month"
  ExpiresByType application/vnd.ms-fontobject "access plus 1 month"

# CSS and JavaScript
  ExpiresByType text/css "access plus 1 year"
  ExpiresByType application/javascript "access plus 1 year"

</IfModule>


# ----------------------------------------------------------------------
# Prevent mobile network providers from modifying your site
# ----------------------------------------------------------------------

# The following header prevents modification of your code over 3G on some
# European providers.
# This is the official 'bypass' suggested by O2 in the UK.

# <IfModule mod_headers.c>
# Header set Cache-Control "no-transform"
# </IfModule>


# ----------------------------------------------------------------------
# ETag removal
# ----------------------------------------------------------------------

# FileETag None is not enough for every server.
<IfModule mod_headers.c>
  Header unset ETag
</IfModule>

# Since we're sending far-future expires, we don't need ETags for
# static content.
# developer.yahoo.com/performance/rules.html#etags
FileETag None


# ----------------------------------------------------------------------
# Stop screen flicker in IE on CSS rollovers
# ----------------------------------------------------------------------

# The following directives stop screen flicker in IE on CSS rollovers - in
# combination with the "ExpiresByType" rules for images (see above).

# BrowserMatch "MSIE" brokenvary=1
# BrowserMatch "Mozilla/4.[0-9]{2}" brokenvary=1
# BrowserMatch "Opera" !brokenvary
# SetEnvIf brokenvary 1 force-no-vary


# ----------------------------------------------------------------------
# Set Keep-Alive Header
# ----------------------------------------------------------------------

# Keep-Alive allows the server to send multiple requests through one
# TCP-connection. Be aware of possible disadvantages of this setting. Turn on
# if you serve a lot of static content.

# <IfModule mod_headers.c>
# Header set Connection Keep-Alive
# </IfModule>


# ----------------------------------------------------------------------
# Cookie setting from iframes
# ----------------------------------------------------------------------

# Allow cookies to be set from iframes (for IE only)
# If needed, specify a path or regex in the Location directive.

# <IfModule mod_headers.c>
# Header set P3P "policyref=\"/w3c/p3p.xml\", CP=\"IDC DSP COR ADM DEVi TAIi PSA PSD IVAi IVDi CONi HIS OUR IND CNT\""
# </IfModule>

Answer 1

The problem is that there are file names which are only differing in the lower case and upper case of file names. This might work if both source and destination systems have file systems that discern lower and upper case, but it definitely doesn't work on file names for example in Windows.