How near is the baby to sexual maturity? Is it at all possible that the father could see the baby as a threat to his previous bond? Trio bonds can be notoriously unstable because one bunny will always get left out. I’ve heard of having to go through the bonding process several times for unstable bonds. It could also be that Daddy bunny isn’t feeling well, is feeling threatened/his stuff is being threatened/space is being threatened and might need reassurance or careful training to realize that his stuff is still his, and nobody will intrude his space when he doesn’t want it. This could also be a sexual maturity thing if the baby bun is marking/claiming things that are already claimed. I’m not for sure on this, but just so you know, male rabbits are neuter-ready at about 3 1/2 (safely)-4 months, much earlier than female rabbits.

You didn’t say how old the baby is. You should not attempt any bonding of rabbits until they all have been spayed or neutered and a few weeks has passed. If this is a young bunny that hasn’t been spayed yet, that may very well be the problem. She may be approaching puberty, and when hormones come flooding in, that can change everything. I assume that your male and your older female are spayed and neutered. You will need to wait until the baby is old enough to have surgery, then try the bonding again after she has recuperated from it. Until then, she should be kept separate from your other two. Rabbits can inflict severe injuries on each other when they fight.

Rabbits can lose their bonds and may or may not regain them. It has never happened to any of my bonded pairs, but I do know people who have had this problem and also have read posts here about bonded rabbits suddenly fighting or not getting along.

Was the baby just recently spayed? Or was the father recently neutered? Perhaps you bonded them before the time was right. You do have to wait for all the hormones to be flushed out, which can take weeks.

Did the father start the first fight too? Is there any possibility that he might have something wrong, like a tooth problem that could be causing pain which could in turn cause aggression? Is he still acting normally with the other female?

If you do a search in the bonding section here, you will see others that have have a break in bonding and what they did to help it or what advice they got.

In the meanwhile, you should keep the baby separate from your other two rabbits, and keep her separate until you have figured out a good course of action to re-bond them.. Rabbits can severely injure each other when fighting. Since I’ve never had this problem, I’m afraid I’m not a lot of help, other than mentioning that you do have to wait few weeks after surgeries to begin bonding. Hopefully, you can either find some answers from similar threads or someone who has gone through this will respond to your post.