Do you know what her circumstances were before she came to live with you? Sometimes trauma is the past, affects their behavior in the future. Have you tried narrowing down what her triggers are? There is usually some sort of pattern.

There are an odd number of parallels between her and my rabbit Fable, haha. I adopted Fable to bond with my Netherland Dwarf, Wick, and that bond did not work out, though Wick is the trouble-maker in the equation; not Fable. Fable is also a rabbit with more bunny-energy than others, in terms of engagement with carpet, baseboards, etc.

There is a difference though, but it may be another parallel. Fable is probably the most anxious rabbit I’ve ever had/interacted with and her expression of that is withdrawing into a loaf, rapid breathing/wheezing, and getting very tense. I say this may be another parallel, as your rabbit may be experiencing that same uneasiness, but has for whatever reason felt more comfortable with lunging/biting as her emotional expression, which is definitely common for rabbits feeling insecure or tense. In addition, Fable was a pretty serial hard-nipper when we got her. Her communication nips… hurt. A lot. Broke skin and I think all my pants have holes in them. It may be a parallel that your rabbit is not biting from aggression, but her orientation of a communication nip has not been given adequate feedback, and therefore is continuing.

One factor that may be present and potentially unpreventable is the presence of another rabbit with whom she’s not bonded. You swap time with the rabbits, and therefore both you and her space is “invaded” by the scent of another rabbit. Rabbits hear/smell before they see, and so if her territorialness/aggression is at all in reaction to his scent, it will be a losing battle for you until that is addressed. What you may be able to try is actually housing them separately, but in proximity, so if it is a scent-based aggression, perhaps she can get accustomed to his scent and not have any reflexive aggression/association with it anymore. In my dynamic with Wick and Fable, Wick was the consistent aggressor and wants nothing to do with Fable, while Fable absolutely loves Wick and is so gentle with him, despite his constant chasing and nips. They both live in our large living room, where one is in the pen enclosure while the other is free-roamed. While initially Wick did a lot of lunging through pen bars and chasing through it in response to Fable’s movements, he eventually habituated and is now completely fine with her presence across a pen wall. This has carried over to him being less reactive towards hands that recently pet Fable.

Re: the potential hard-communication nips, you can try providing feedback that hey, communicating your needs that way is not OK. If you are going away every time she bites (which is a natural response of course!), that is reinforcing that is the method she must use every time she wants anyone to leave her alone– it is effective in getting those hands, feets, legs, etc. to go away, so why stop? Doing a high-pitched squeal each time it happens can provide feedback that “hey, that hurt”, in addition to gently pushing her head away with the backside of your hand (typically more smooth and less likely for a rabbit to nip than the palm of your hand), approaching and pushing the head from the side (not front). I did this repeatedly with Fable so my hand would essentially turn her body so she’d hop away. My interpretation, and what I hope she got from this consistent feedback (squeal and gently turning) was, “Hey, this hurts, and you should go away. Don’t communicate with me like this because I’m not going to listen to you.” Once she does a nose nudge or a less intense nip, then I’d go away.

Just confirming that she is spayed?? You may want to double check with the shelter and have them pull her spay records, because mistakes can happen!

I agree that the scent of another rabbit in the area who she isn’t bonded with might be upsetting. To me she sounds “cage aggressive”, although I know she isn’t locked in a cage, she could have been a bit traumatized from her past before you got her. Can you describe her full housing set up? And how often do you have to pick her up? I think there can be such a thing as too much space for some rabbits, they feel the need to defend EVERYTHING, and you coming in to the room to spend time with her might be seen as an invasion (as opposed to maybe having a pen in that room be her space, and then you open the pen when you want to spend time with her).

This thread might have some useful tips:

How to Deal with an Aggressive Rabbit

I also wonder if you might be able to do some clicker training with her to break some of these behavior patterns. Since she is already taking a treat from you, that’s a great start. The main idea is think about the behavior you want to see (not what you don’t want), and then train that behavior. So perhaps instead of her lunging at you, you could train her to go to a mat where she gets a treat. The basic idea of this is laid out here (this is a dog trainer I love but the concept is the same): https://www.youtube.com/watch?v=6vAk98000wc&list=PLXtcKXk-QWojGYcl1NCg5UA5geEnmpx4a&index=22&ab_channel=DogTrainingbyKikopup

There is also this technique used in dog training that involves “capturing calmness”, I wonder if it could be applied with her? https://www.youtube.com/watch?v=wesm2OpE_2c&ab_channel=DogTrainingbyKikopup

OK, if the triggers are simply you entering her space and not something more specific, then I agree with the others. She may be feeling she needs to defend her entire area, which can be very stressful.