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I am very sorry for the problems you're experiencing. Please send me a Private Message (the 
in the upper right-hand corner of the forum) with any Customer Support ID numbers so we can contact the technician about the issue of file removal.
As for the issue of the file limit for File & Folder Backup, how are you seeing this issue? Are you able to create a backup job for the files, but when it run, there are errors? Ghost reports all warnings and errors to the Windows Event log. Could you look at the application event logs and check for any warnings/errors from Ghost, Ghost Service, V2i, Volume Shadow Copy Service, etc? Have you run LiveUpdate in Ghost until there are no more updates? Any additional information you can provide is appreciated.