When you moved them in to there shared area did you deep clean and re-arrange it? A lot of rabbits after being bonded need to cement in a “new” neutral area. This can be accomplished by the cleaning/re-arranging. How did you go about bonding them originally?

Since you took a break from bonding you might need to take steps backward to move forward. I might even start completely over and see how things go. Try some sessions in a neutral area and see how they get along. If they are having the same problems work on them there before moving forward to semi neutral and so on. Going back to the beginning will show you what stage their relationship is at in the process and where they need work.

I understand a bit better. I think the shared play time involving their cages is/was the issue. You really can’t just combine current cages/space while bonding rabbits. As you saw, it leads to territorial problems.

I would continue doing sessions until they get along in semi neutral space. After that I would move on to cementing. Cementing is the last stage of bonding . You start by preparing an area that will be their shared home by deep cleaning and moving stuff around to make it as “new” as possible. You then put the rabbits in the area and supervise them until they get along for 24-48 hours. After that they’re considered bonded. This time needs to be 100% supervised and the rabbits should not be separated unless you are worried about serious injuries. Instead of separating when/if a fights arise it’s better to stress bond them and return them to the cementing session. Anytime you have to intervene the 24-48 hours “resets”.