the savestates will still work, as long as the name of the rom is the same. just rename the file to the name of the previous rom. make sure to use the same punctuation and spelling.
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.