Ok, so I have been having MAJOR issues with my two since I bonded them. They were bonded 6 months, all through that they didn’t use their litter boxes and I couldn’t get them to at all. Then they broke up for 2 months, same day they broke up and I had to separate them, they went to 100% litter habits again. Then Powder rebonded himself to Stickers, just one day “I want my girlfriend back” and broke in and they snuggled and he groomed her and they haven’t been apart again since. But they went back to not using the litter boxes. Top it off, Stickers is destructive, so she’s been eating carpet/digging/chewing furniture and being a total brat. When not bonded, she responds to me telling her to stop. Bonded, even a spray bottle won’t stop her. Ugh.
I tried confining them in their room, made it worse (I even have a nice hole in my flat plaster wall thanks to that lol). Tried giving them space, made it a little better, but still not quite. So it’s been about 8 months now of experimenting with different layouts, freedoms, food schedules, toy rotations, litter box cleaning frequency, hay placements… lets just say 8 months really hard work. lol (Both of them solo equals about 1/8 of the work the two bonded has been)
BUT … I found it. Finally. I have baby gates set up in my computer room, which is attached to the hallway, which is attached to their room. I left the entrance of my room and about one large X-pen sized area beyond the door open to them. The rest is gated off. If I leave that part of my room, their room and the hallway open to them, they use their litter boxes AND she listens to me. Any more and they go nuts, any less and they go nuts.
Do I have the worlds pickiest bunny pair or what? 
Edit: Oh yeah and their food has to be spaced out over the day, their hay has to be freshened 2x a day, Stickers needs one litter box UP IN THE AIR on top of a plastic container and there can only be BROME hay in the litter boxes themselves, the treat hays must be out on a plate. Veggies must be given 2x a day. If all this is carefully scheduled and done properly, I have two very well behaved bunnies. Anything amiss and she enters destruction mode, or marking mode.