I divide the room in half using an “x-pen” that is folded so that there is space between the two areas. You need to make very sure they cannot nip each other through the fence. If that sort of set up isn’t possible, then yes, you will have to exercise them one at a time, but make very sure the one that is out playing can’t harass the one in the cage. You can use a pen or something similar to make a space between the cage and the play area.
Usually 5 inches buffer is enough.
I think letting them play at the same time is preferred if you can, so the one that’s caged doesn’t get frustrated at the other rabbit running around “his” territory, plus both bunnies get more play time this way.
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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.