To be honest Archer never had a problem with Cobra. Even in the beginning he was okay putting up with Cobra AND NOW THEY'RE FRIENDS not that he'd ever admit it because Archer's dumb as hell.

ALSO I KIND OF WANT TO SNAG A COBRAMON FOR NAKI are there any of Cobra's Pokémon you'd like to keep around? I've got no real preferences, so if you've got any hilarious ones Naki can be stuck with them!