what do you mean by don't save? does the data from saving not load properly when you hit continue?does it say to exchange the backup memory? do savestates not work any more? I need more detail before I know what the problem is. send me a video, or something.
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the battery file is either a .bat or a .sav, so if there are any files like that, move them into a different folder.
.bat files for me, have a description of "BrainBreaker_SavedPuzzle" so that is also a battery file. don't delete them until you're sure it worked though.