So sorry this happened, how stressful
My vet doesn’t let bonded pairs stay together either, and they are the best rabbit vet in town (our rescue uses them, so they see TONs of bunnies). They say that they need to separate anyway to observe poop (which I completely get), and most of the time bonds don’t break (which I believe, since they see so many). Plus, even if you had brought them together, no guarantees. Member Sirius&Luna’s trio just all went to the vet together and stayed together, and they still had issues.
So, don’t beat yourself up, these things happen, even when you do everything that’s recommended. It’s unclear whether it’s a new location, new smells, other rabbit smells, or the illness of one bunny that triggers these things, maybe some combo. Illness and medications can make buns smell differently, and behave differently. Hard to tell what’s goin on in those bunny brains…
I would keep them side by side, just like during pre-bonding, while Zoe finishes her stasis treatment. You can even start swapping litter boxes, and petting them both to swap scents. Zoe will be happy to see Simba, even if he isn’t so sure about her.
Once Zoe is better, start up the bonding process and see how they do. If they do well, you might be able to just go straight to marathoning in neutral, but you’ll need to judge their behavior. It’s quite possible that once she is doing better he will react better towards her.
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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.