Make sure that if they are PINE shavings to find another litter – you can even use pine pellets, but the shavings are not good for rabbits.
I think what you should do is try to make her box inviting. Add some hay and treats.
Also, if you are finding she’s using it for a lounge area, then what does she have right now for bedding/lounge area?
The other thing is if she is unable to get out to exercise, she might be just getting out some excess energy by moving things around. I know your husband seems to be afraid of germs or whatever, but keeping her locked up just can’t be the final solution. As a compromise with your husband’s bunnygermaphobia and your bunny’s need to exercise, why not attach an xpen to her cage? That way she can get out and stretch her legs, but for right now, while you are littertraining her she can still say somewhat confined. Though in the future, your husband will have to get over his fear in order for your bunny to have a better life. Rabbits are actually very clean themselves. What in the world is he afraid of getting?