Vet visits can actually set off fighting even with fully bonded pairs. The reason is after a bunny has been at the vet, they don't smell the same to the other bunny. One tip in the future is to bring both bunnies to the vet even when only one is seen.
So if he came home smelling different, she may feel the need to go through the whole dominance dance thing and he is thinking....what the....haven't we been through this?!!! So this can cause some major problems.
Bunnies can even sometimes still fight even if they went to and from the vet together. Especially if their relationship is rather new. So it's a good idea as soon as you get home to pet them both and rub each other's scent on each other.
For now, you may have to start over.
. I know....I know....awful!!!!! But give them a few days apart to relax, and then begin again. It may not be as hard the second time around, but I do understand that this setback is more than just a pain in the arse. This happened to my original bonded pair, so I understand the complete frustration.
If they continue to make zero progression, you may have to wait until their completely done with their meds as that can make them smell different too.
Good Luck! Keep us updated. I'm sending new bonding vibes their way!