osh man, it corrupted part of your card, or at least something did. I had that happen all the time with my SCSD, altho it wasnt because of an app, it was due to the saving method of its built in emulators. youre just lucky it didnt delete everything.
try to run it through a data recovery program. I salvaged a lot of .sav files with that. :\
and btw it always had a file that was bigger than my card and had a weird name too, thats a tell tale sign that the card's data is corrupt. id back up everything else off of the card asap if i were you, reformat it (but not before using a data recovery app), and then put everything back on.