They might, it depends on how much of the ROM changes. To be really safe, always save state in a Pokémon Center before you update the ROM - I VERY rarely edit the PCs, so they are safe places to save state and won't glitch if you reload after changing the ROM.
Sorry dude, that's a well-known bug and I've not been able to fix it. If you use VisualBoy Advance, you can use an alternative, save states. Where you would normally save, do Shift + F1 through to F9, giving you nine slots for your save save. Then, when you load the ROM, hit the F number that you saved most recently to, in order to reload your save. Sorry about that dude.