AHA! I knew I wasn't crazy!
Ogre, the problem is with the game. This exact same thing happened to me recently. Your other files are gone forever. I recommend getting a Tennokoe Bank cart (kind of like a back-up memory card) and keeping the Shape Shifter save file completely isolated in it's own "Bank" on this card, away from your normal saves. That's what I ended up doing because I am not willing to risk losing my other files again.
I had some high score lists that were at least a decade old that were lost when Shape Shifter decided to hijack my save memory.