This is definately a major issue that your webhost provider should have fixed much more quickly than they have, infact they are clearly doing something to the filetree that they should not be touching in the first place.
As for automating this with FlashFXP, i think MxxCon isn't quite accurate saying that it can not be done as this depends entirely on the webhost itself. FlashFXP now supports command queueing, so if you can log into the webhost via ftp/sftp and issue the commands manually (raw command), then you can absolutely do it automatically as well. Create a .fqf file containing the commands you need to send, then create a windows shedule to launch FlashFXP (using its command line switches to auto log in and run the .fqf file) every X period of time and you should be set.
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