I have had to do this before, and most times it works out fine. I’ve never had an upset and have had to do this with multiple pairs because my vet has told me they would separate them at the vet anyway to monitor poop. Sometimes even after prolonged separation the bunnies are very happy to see each other and will greet each other like “OMG I MISSED YOU”.
I would bring them home in the same carrier, and you can rub a towel over both bunnies to mix their scents. You might bring a spare carrier just in case but they will most likely be fine in the carrier. I would plan to keep an eye on them for a few hours afterwards, chances are if there’s an issue you will know right away. If there is an issue, they usually will go back together pretty easily as long as they don’t get into a major fight.
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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.