the problem isn't set in stone, just very hard to undo (written on the stone with chalk, if you will). open SG, hold shift and press F1. now delete your save file. load the game, and press F1 at the title screen. now make sure the save settings are correct. if they are, save the game.
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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I moved it to a different folder (within the Visual Boy's folder) and it didn't do anything. How about the .sgm file? Should I move that. I'm starting to think my FR rom is FUBAR. If I get a new ROM can use the same save state?
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.