A very similar thing happened to me twice last week, mainly during the installation of quantum theory my ps3 crashed so i tried to delete the "partial installation" as requested by my game, so i tried and it left a corrupt 0kb file in my installation folder.
So i left it, later that night i was watching an episode of south park on my ps3 and it crashed again, rebooted itself and rebuilt database, that removed all my corrupt data and retained everything else, the bad part was that less than 12 hours later it crashed again (playing a backup) rebooted and said it needed to rebuild database, so i thought, ok no worries, go for it, IT FAILED :'( I then had to reformat my hdd, FAILED.
I had to remove my hdd, put it in my phat ps3 to reformat it, then put it back in my slim, reformat again (worked this time) but I lost everything, obviousley, now my concern is that it will do it again, so every night I backup anything thats changed on my ps3, mainly saves to a mem stick via multiman just incase, also my trophies dont sync anymore, its a right pain in the ass.
Bassicaly, this can occur at anytime and I highly recomend backing up anything you dont want to lose regularly through multiman or an ftp server whichever you prefer.
Now im off to so a complete system restore to fix my trophy problem and re-do my kmeaw blah blah
EDIT: FOR THE OP!!! if you go into the recovery menu (only recomended if your on 3.55 or lower) you can force the ps3 to rebuild your database deleting any corrupt data, however, this is fairly big so pay attention! IF ANY ERROR OCCURS YOU COULD LOSE EVERYTHING! so backup whatever you want to keep if you do go ahead and try it, its worked for me before but can always cause an error.
I take no responsibilty if you do try it and it errors out and you lose everything, especially if you didnt back it up.