For a while only two of my five rabbits were bonded. It can be a challenge but I think it’s doable if you coordinate with each other.
A couple ideas:
1. A rotating schedule. Maybe certain times of day or every other day one of the bunnies is “prioritized” for exercise time. One bunny could get mornings and the other could get evenings. Or one bunny gets first choice of times one day and the other the next. This doesn’t mean you guys couldn’t bring them out when the other person isn’t home or the other bunny is not out for whatever reason. Just that one gets first pick on that day or time period. Does that make sense at all? O.o
2. Can you bunny proof your room for exercise time? This could be a way to give her more time out on days/times she can’t be in the common areas.
3. Depending on the size of your place could you split the common area in half with a barrier of some kind, maybe NIC or X Pen, and give each bunny half for exercise? Something you can portable that you can easily take down and put up when needed. You can place cardboard, a blanket, or some kind of cover over the barrier to keep them from seeing each other/fighting. This is actually my advice for the cage issues as well. Covering the cage or placing cardboard around the bottom part of a cage while the other is out.
I know it probably sounds like a troublesome amount of stuff to do or figure out but I think if you can work out something it will become easier with time. I hope others pop in with more advice/ideas. I hope everything works out and please do keep us posted 