As I recall it, if you run on
Autosave, it'll save over your existing data. That should be turned
off. But I've also heard and read about people who had their
entire save files go missing.....So that one is harder to fix..
Don't have much to go on except that
start by uninstalling and reinstalling the Skyrim Game Data (not
Save Data), then perform the PS3 file system restore. Haven't done it myself, but I hope this link provides some info to this:
http://community.us.playstation.com/t5/PlayStation-Home-Support/Restoring-your-PS3-File-System-Database-Helps-to-Maintain-PS3/td-p/37322987
Hope it helps.