Check on the SI forum. Maybe they can help. A lot of these issues are caused by an Anti-Virus program running system scans while FM is running, so make sure it doesn't next time.
Switching off the scans after your save became corrupt won't help, if I understood you correctly. It will help with any future save though. As a matter of caution always select to have a 3/5 file rolling save. Then you'd have backups automatically too.I know, switched all my anti-virus off but the problem still persists.