This has not happened to me, but it is scary.
seems that something happened to that file. What says the log in the admin site?
did You open that file using FileMaker Pro? Did it say 'consisteny check' (or similar)?
was there a network issue, a power failure while writing/developing (client side)
You should be able to trace it through the FMS event log... at some point the file must have been closed so there should be an entry.
I had to go back to a 3 day old daily backup, send it over to a client machine, and upload to server via FMP.
If you are already on the server looking at the backups, you don't need to send the file to a client machine just to upload it to the server again. Just copy (never move!) the file from the backups folder to the live folder. On OSX, then set the permissions on the file (Windows does not require this). If you are not comfortable with the OSX command line then use a utility like BatchMod to set the permissions.
This is usually faster and less change that the file gets damaged in the up and down transport.