Set backs are tough – mine had a couple mild fights over a month after moving in together.

For now I’d go back to what you were doing before – let them get comfortable just playing together in the evenings. When you feel comfortable again, move them in together but make sure to spend the whole night on the couch so you can be there to break up any scuffles. Also, the set up of the cage is important. Instead of putting them together in a cage that one used to inhabit, set up a new area with completely clean things and no hidey spaces they can be territorial of. This phase is called “cementing” and it’s a chance for them to live in a fairly small space together with nothing to fight over so they finally get used to the idea of living together.

Since mine were only bad at night/early morning, I started having them sleep in a small pet store cage so Hannah couldn’t chase Otto. I also brought the cage into my bedroom every night so I could hear if they had a fight. I did this for probably 2-4 weeks before introducing them to their big cage for the whole night.

I found the pecking order changed throughout bonding. It seemed that Hannah was definitely in charge at first – she humped all the time and constantly demanded grooming (which isn’t surprising since she has a dominant personality in general). Strangely, when they moved into the cementing phase Otto started humping her! It was very weird. He even still tries to do it occasionally even though she’s clearly in charge and chases him away from food or treats (she doesn’t hump him anymore, but only because he runs away too quickly). She’s in charge, but she became less dominant and he became less submissive when they were fully bonded.

My theory is that dominance in rabbits isn’t all or nothing. To live together as a unit they all have to groom each other and make sure the others get enough to eat. In the beginning one rabbit might want to be super dominant, but eventually they need to learn to do things for each other because that’s how rabbits survive in the wild together. I think this might cause the flip flop as the submissive rabbit realizes that he wants to be groomed too.

I think it’s ok to use the same cage as long as you clean it really well with vinegar. Can you move it to another spot? A change of scenery might help too. Mine lived in the dining room, but for cementing they moved to the living room (and later spent nights in my bedroom) so it seemed like a different set up at least even though the cages and pens weren’t new (once they were bonded in the new areas I moved it all back to the dining room and they were fine)