Our two rabbits, Kenobi and Yoda (or Nobi and Yodi as I call them), used to hate each other. We had to keep them seperated. When we first moved here, we were keeping Yodi in the bedroom in a cage and letting him out when we were home, with the bedroom door shut. Nobi was a free-range bunny who had the run of the place but usually hung out in the den.
Then Yodi destroyed one too many alarm clocks and books (not to mention carpets, walls, furniture, electrical cords, clothes…) and we put him in a dog pen in the living room. After that, Nobi started hanging out by Yodi’s pen. They would lay next to each other and Yodi would groom Nobi though the pen. Due to various reasons, we decided to put Nobi in the pen too (he never left that area anymore anyway). At first they fought but now they’re best friends, except at treat time. Then they push each other out of the way to get to the treats. They like to lay next to each other and Yodi still grooms Nobi. They seem happy together now.
We do need to start letting them out more often to run around (supervised) but we have to Yodi-proof the living room better. There’s some cords and other things that he could get to easily right now.