the neogeo has a battery for the clock and game settings.and...when you load a new game, you unload that configuration. But I'm afraid that AFAIK the configs/records are stored in the Motherboard itself. Am I right?
but we're not talking about game settings, we're talking about the flash cart settings, and then just which game is loaded.
a simple text config file on the microsd card would be enough. on boot the ARM checks for the file, if present it boots whatever game is listed. when a new game is flashed the ARM re-writes the config file for the current game just before the auto-reset.