I would look at your DB back ups and compare the table size from now and the last back up. If the ost_file and ost_file_chunk tables. ost_file has general file name information (size, name, date, etc), ost_file_chunk has the actual files. I'd restore from backup, because it sounds like your server had an issue with the file_chunk table. You might want to look at your MySQL error logs to see what that issue was.