Backup your save states(e.g. on your pc). Then download the 3.6.1 patch and use it to patch on a firered 1.0 clean rom. Then delete your current 4.0/4.1 beta .gba game. Then rename the patched game(Ash Gray 3.6.1) so that it´s exactly like the save states you have(e.g: name of your patched game: Ash Gray.gba; name of your save state: Ash Gray.sav). Then continue the game to that point . I suggest that you go inside a building and save(ingame and/or save state of emulator). Then delete Ash Gray 3.6.1.gba game and now patch Ash Gray 4.x on a clean firered rom. Make sure to rename your Ash 4.x like your save state. Then you can continue to play.
Hope this helps