Spaying, if she isn’t already would be the first step. Plus girl bunnies are prone to cancer if not spayed, so it’s a good idea for health firstly..and then you also get the benefit of better potty habits. As my vet says..any behavioral issues he doesn’t care about…but we better do right for her health since that is his concern.
How is your box set up? Willow is very specific about her set up. The box has to be large enough to easily fit her whole body in. She wants a thin layer of wood pellets and then hay over that.
She is 100% as long as it’s set up like that. Any deviation and she will potty elsewhere. She does not like a hay bin outside the box..the hay needs to be in the box. She does not like her pellets or water any where near it.
Not to say this is exactly what your bunny wants, but my point would be that each bunny is an individual and may have certain requirements about his potty place. You may have to do some trial and error till you get his approval. Try different boxes, both style and size, different litters, try moving it to different locations.
Our bunny is mostly free roam and then penned at night. While potty training her we had her limited to the kitchen. With having the whole house she has a box in her pen, one in our bedroom and one in the bathroom. She uses the one in the bathroom most. She seems to think bathroom time is a group activity.
Good luck!