If the list is not updating then just delete the map file based off the emulator number. The number can be obtained in Emulator Setup. It's the number next to the name. And the map files are in the DATA directory. So if it's emulator 1 then you would delete the EMU_2.map file and the list will updated. To answer your other question, yes just put in the filter so that those files don't show up. Emulators usually give you an option on where to save the save game files so that this won't be an issue.