I guess a bit of a backstory is in order.
So last June I adopted my first pair of house bunnies called Janus and Bilby. Two 6 month old neutered males that are brothers and were supposed to be super good together and were only adoptable as a pair. First after I got them there was a bit of fighting (stress because of the move and only a week after they were neutered) but it quickly settled down. Every once in a while I would find a chunk of fur from Bilby but never from Janus. This slowly got worse and I would start seeing Janus chasing after Bilby and nipping at him. At the same time Janus was overgrooming Bilby to the point where Bilby had no whiskers and was starting to get bald spots around his eyes.
In January I got a female rabbit, Gizmo, to try to balance the relationship between the two, but was only giving them short sessions together since Gizmo wasn’t spayed. One day that month I was checking Bilby’s fur and noticed several spots in his coat where the fur was very short (maybe 1-3 mm) the size of my thumb. I was very shocked and realized the stress Bilby must be under with the abuse from his brother and separated the two after getting advise from here.
In February I spayed the female and kept the three separated but in the same room (Janus in a cage, Gizmo in a pen and Bilby roaming free). When the month went on I started rotating which one was where so they could get used to each other’s smell and each could get some time free. I also let Janus and Bilby run free together every other day, but only under supervision and not for long time.
In the beginning of March I really started really focusing on bonding Bilby and Gizmo and she really is perfect for him. He is a bit skittish and nipped a bit at first, but she is super forgiving and very sweet so once I put them in my bedroom for two weeks in adjoining pens I took the plunge and joined the two permanently (still in my bedroom just in case). It took maybe 12 hours for them to start to eat and cuddle together and for Bilby to completely stop nipping at Gizmo.
Meanwhile Janus was in the living room mostly in his cage but got to run free under supervision.
I always felt bad for Janus being all alone in the room, so today I let him come into the bedroom with his cage (he was free, Bilby and Gizmo were in their pen). It was horrible.
When Janus realized his cage was open, he started by stomping and growling while jumping towards the pen. Then both Janus and Bilby were simply tails up, ears back and then they started lunging at each other. Poop was flying, paws were pouncing, there was growling and biting and I was so relived that there were bars between them ’cause this was simply horrible. They were clearly in some sort of fighting stance that I have never seen before (and closest thing I found on youtube was a video of wild rabbits fighting). I of course put Janus back in his cage and after seeing Bilby on an obvious lookout, I put Janus’ cage back to the living room.
Now what should I do? Is there hope for Janus and Bilby? I feel super bad for Janus for beeing alone (he doesn’t seem very happy) but the stress he is putting on Bilby isn’t acceptable. I also don’t like Janus’ cage to be a permanent solution, and it was never intended to be.