Rabbits who have not yet reached the hormonal, puberty stages of growth often get along with other rabbits easily. It is likely this, rather than them being related that allowed them to get along. Rabbits do not acknowledge family units like we do — they will fight and mate with siblings and parents all the same, so the progression you are experiencing (i.e. they were getting along and now they are fighting) is actually quite normal and is to be expected now that they are older.

“Is this even possible to bond them now?” – Arguably, I’d say this marks when you can actually start bonding them. If you wanted to be extra cautious, you can wait a bit so there are no lingering effects of the neuter (post-neuter ‘craze’ as they call it) and to ensure there are no leftover grudges from previous negative interactions. For rabbits who were unable to get along post-puberty (which is a big portion of them, as yours did), you cannot start bonding until they are all spayed/neutered, since the procedure helps mitigate some of the challenges in creating lifelong bonds. That being said, neutering/spaying is not a magic fix — rabbits will still likely be territorial and aggressive, as you are seeing. Again, this is common and not surprising.

There is general information about the rabbit bonding process in the RABBIT INFO section of this website. It will start with introductions in neutral territory only (no where they have free-roamed themselves and claimed as their own space), as well as pre-bonding measures, like swapping what pens they are staying in or swapping their litter boxes and toys.

Echo everything Wick said, and I would also wait until your female is spayed and all the babies are gone. Having a hormonal rabbit around can definitely complicate things, even in fully bonded pairs. I once had an unneutered male in my bathroom overnight (I was taking him to the rescue in the morning), and my bonded pair was FREAKING out. So smell alone can def mess things up!

When they fought, how bad was it? Did any of the buns get so injured that they needed medical attention?  Bunnies can hold grudges, so if one was badly injured, it may be hard to bond them, especially in a trio. Maybe you could do two pairs (two males that get along the best, and then your female and the third male)?

When you’ve tried the boys together, what was the space like? Was it super neutral?