...no details? Helping the obscure is a little difficult.
I had Fallout 3 autosave over a separate, manual save file (which it shouldn't do, the autosave file should exist for that purpose). Twice. Second time I lost my favourite character and 100+ hours of gameplay
Oh yeah, sorry for the lack of help...I was playing PS3 GOTY so if you're the same I'd say it could be a bug. If not...well, some of the other guys might be able to help.