My suggestion would be what someone said earlier in the thread, go to the new region, get to where you've got some Pokémon at or just below level 60, then come back to hoenn to beat up the elite 4 with those.
I know being forced to do that kinda sucks, but just keep in mind it was just very unfortunate timing for you and other people in the middle of the story when the update hit. Redoing the mechanics again just to fix an issue only these certain people will ever have doesn't really make sense. Once the people it currently affects can get through it the problem won't exist for people again in the future.