Hold on... .BAK?
I'm not familiar with this extension. Is that just how you rename files to keep them as backups? (Me, I just copy them indifferent folders) Or did I completely miss a file type the emulator uses?
Anyway, I do still have the back up and I'm certain it has the same name as the game since I didn't change the name at all and when I tried copying it back into the games' folder and booting it up to then save some changes from the otherwise default appearence of the game, the copied file went from being 8mb to 400kb... so yeah, it definitely was overwritten.
Really weird, isn't it?