Hi Emma,
I moved this thread to the bonding section, as it is more relevant to the topic.
Sorry you are experiencing this, I’m sure it is very stressful. 🙁 It should be possible to repair their relationship, but you did the right thing by separating them. Was either bunny injured?
For now give them some cooling off time, which will also allow your boy’s hormones to settle. The fighting was most likely because the boy now smells different because his hormones are changing.
A couple of questions. First, are your rabbits babies? And is the female spayed? I ask because baby rabbits get a long, but do not truly bond, and your female hitting puberty could also be affecting things.
If they were not babies, I’m assuming the female is spayed? If that’s the case, the path forward is a bit simpler, and you will want to let them cool down for a few weeks, then start pre-bonding, and go through the bonding process with them. He will likely smell very different so hopefully she won’t react the same way after some time passes. If she’s not spayed, you’ll want to get her spayed, let her hormones settle (usually several weeks), then go through the same process.
NIC cube grids and dog kennels can be used to make temporary housing for during this process.
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.