So, this just happened:
Got to the E4 in Unova, couldn't beat them. Decided to raise a couple new mons in Kanto to make a more diverse team.
Started Kanto, raised some stuff to complement my strongest Unova mons. When I beat 8 gyms, got out my Unova guys and completed my team.
Beat the E4 in Kanto, feeling good! In the process, 4 of my mons reached lvl 57. Didn't think anything of it.
Right! Back to Unova, let's take on the E4!
I think you can guess what happened. There's no (in-game) way I could have known that all these pokemon would be disobedient and immediately die at the beginning of each battle. It's not like I'm using OP pokemon to blitz through the story in a new region, I just need to beat the E4 in Unova. It seems totally unfair that this situation is even possible. I get that allowing players to use lvl 100 pokemon at the start of a region is silly, but I just spent three days finishing the story in Kanto as a fun way to get a better team for Unova E4 and now I can't use them?
Is there no way I can get my mons back in Unova? I seriously need to raise 4 new pokemon from scratch just to beat the E4 there?