I'm not sure if anyone will be able to offer any brilliant solutions, but I figure it's worth asking and getting it out there. Sorry this is long.

Hannah still has problems with humping, nipping, and chasing Otto at night - badly, and frantically. We have kept them in a 3.5'x1.5' cage every night for a month (this is Hannah's old cage) and they are fine in there. I'm happy we at least have a safe place where I know she'll behave.

Two nights ago we tried to move them into a 4'x2' cage, to give them more room, hoping to eventually allow them the whole 4'x8' pen. The first night she was fine, as far as we know, though she pooped everywhere, which isn't like her. The second night, she started going after Otto within seconds of me shutting the door. A little humping is fine, but she really launches herself at him frantically and I know her chasing him will cause him to retaliate. It's one thing when we're around, but since this happens at 5am usually, I know I won't be able to sleep if they're already not getting along at bedtime. We put them back in the little cage and she was fine again. They haven't spent many nights in the big cage, but it's open all day and the litter box is in there, so she's comfortable going in and out, and spending time chilling in there with Otto during the day.

I think part of it is displaced aggression - the new cage (even though she goes in it every day, just doesn't sleep there) made her nervous, and she went after Otto. But I'm not sure why being locked in the big pen area (they get locked in there during the day frequently) would cause chasing and issues. She seems to become much more territorial of food when they are locked in any area other than the small cage (she doesn't do this at breakfast for some reason, which is fed in the large pen - only at dinner time).

I'm tempted to just go from the little cage to the pen, since obviously the big cage isn't working for her. But I'm still worried about how she'll react in the big pen, considering her over the top reaction when we took the little cage away this week. Both cages are positioned in the pen area, so the location isn't changing.

Will she ever be comfortable living in the big pen with Otto? Does anyone have a similar experience with recently bonded (2 months ago) buns? I always hoped that their relationship would grow out of this with more cementing, but it seems to come back up whenever we move them out of the little cage. Having two bunnies in a tiny cage like that every night just isn't a long term solution I'm comfortable with.

At the moment, keeping them in the small cage at night seems to be our only option anyway, since it's the only place we can trust her to behave. We'll just keep using it for a while I guess. It's just so so small - they literally only have room to make one hop once you factor in a litter box and hay rack.

But what is the best way to transition her out of it? I'm not sure how we'll know she's ready, since they've been sleeping in there for a month now and I thought she would be ready, but she's not. My newest idea for transitioning her is to feed them in the small cage as usual, but not shut the door and just leave it open to the pen area. She might feel comfortable because the routine is the same and the cage is the same, but it will allow them to come out and move around as well.

Also, she's been living here for 3 months, and living with Otto full time for 2.5 months. I didn't make that clear before and I kind of forgot how long we have had her.

And I totally agree with you, Sarita, that it's related to stress and tension. I think she is very sensitive and new things make her nervous, so I'm wondering how to make her less nervous about a new area. If time is all she needs, that's fine, but I haven't seen her improve at all in the last 2.5 months.

My newest idea for transitioning her is to feed them in the small cage as usual, but not shut the door and just leave it open to the pen area. She might feel comfortable because the routine is the same and the cage is the same, but it will allow them to come out and move around as well.

The best hidey spot we have is the maze haven, but Otto tends to run in circles and not hide. He needs to get the hang of that. We could probably get some more boxes and made more hidey spaces with those. She's very fast and gets very into it, so if he doesn't hide and just runs around, she can easily keep up with him, nipping his bum along the way. He rarely stops long enough for her to hump him.

When they're in the 4'x2' cage, there's obviously nowhere to hide, which is why it makes me nervous. They just go around and around. At least in the full pen, I can set up other hidey areas. I agree that she doesn't do this during playtime because there's a large territory and they're not locked up at all. She will chase him away in the living room, especially if I have treats, she'll nudge him away so she gets more, but she is never frantic about it and Otto doesn't get scared by it. It's only in the cage that she goes over the top a bit.

I'll work on making more hidey areas before moving them to the pen again. I don't think we'll lock them up in the big cage again, because it seems to provide just enough space to chase, but no room to hide.

I also think she is best in the small cage, because that was her cage for 3 years - she feels comfortable there and knows without a doubt that it is her territory. In the big cage, she left about 20 poops in less than 5 minutes, so I think she feels the need to claim it (only when she's confined to it, since she goes in and out of it all day long and never leaves stray poops).