Hi Laura,
I’m a bit unclear on your timeline, but it sounds like you brought the new rabbit home, and immediately started bonding. It’s really important to give a new bunny at least 2 weeks to settle in, as often they don’t feel comfortable in a new place, so they submit to the old bunny, and you don’t see their true personality. Then, when they feel at home a few weeks later, they’re ready to assert themselves and fights start happening.
It also sounds like you rushed the bonding process a bit. I would check out the BUNNY INFO section on bonding for an overview of the steps,but I’ll summarise below.
1. Let new bunny settle in for two weeks
2. Start prebonding – swapping between cages every other day
3. After a month of prebonding, introduce on neutral territory
4. Slowly increase the time they spend together, intervening to stop any fights
5. Look out for positive behaviour like grooming each other and flopping together. Work up to 8 hour sessions together.
6. Monitor them for 48 hours straight in their permanent home – if there are no problems and they’re grooming each other, snuggling, and sharing food, they’re bonded.