Hello 🙂
So, you already mentioned the most important thing, patience. 🙂 How long have you been working with them so far? Did you do any prebonding to help them acclimate to each other?
From what you describe, there is a good chance your current strategy will work with a bit more time, if their behavior isn’t getting worse over time (sounds like once you removed the litter box things got better again?).
There are lots of different approaches. I think if I were you, and I wanted to keep working with them in the small space, I would work on building trust a bit more by petting them both lots and keeping them very calm. When one bunny approaches the other, pet pet pet to make them think they are getting groomed. When one asks the other for grooms, pet pet pet them both. You don’t want to get in a cycle of them getting frustrated with each other and becoming fearful. Eventually you will need to ease off the petting, but I have had a lot of success with this strategy.
Also remember every pair is different, so what worked for you last pair might not always be the best. I tend to like to do some short dates before marathoning, to get the point where they at least seem calm around each other before launching into the overnights. Don’t be afraid to give them some breaks if they seem like they are just getting frustrated. It won’t undo any progress you’ve made. With my most recent two, I started a marathon, then realized it wasn’t getting anywhere in the current space (each night they would scuffle, and each night was getting a bit worse even though they were cuddling during the day), so I gave them a day off to rest, and then restarted the marathoning in a new space that evening.
Litter boxes can cause disputes early on, so I tend to use a layer of puppy pee pads with tons of hay on top, rather than an enclosed box.
Personally, for marathoning, I have had much better success with a very large space (like 2 x-pens linked up). If disputes happen, I’ve found they are less likely to escalate because they can get away from each other. When animals are afraid the options are fight or flight, so if they have no option to flee they will fight. So if this an option for you, you might try that as well.
But if that’s not an option, nothing you are doing sounds like it’s going too horribly. As long as both bunnies are eating and pooping normally, and fights are not increasing in severity or frequency then you will likely get there with the current plan. If you want to try a larger space again I say go for it (as long as it’s neutral), just don’t add a litter box just yet. I usually hold off on that until they seem almost bonded.
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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.