It sounds territorial. Very reminiscent of my duels with Wick.
I find for Wick, not having access to something he thinks he should/sees other people do but he doesn’t is a big point of contention for him. He’ll pee and poop all over the obstacle. Some areas in my old apartment would take longer for him to realize. He realized it quickly with the closet door in the bedroom, so he started peeing there, but it took him longest with the office. It was his way of saying “I want in. Give me.”
Based on this, it makes sense that your rabbit expressed frustration at getting limited to downstairs. He was initially frustrated that he couldn’t go very far upstairs, but now you’ve taken away territory he had already established was his (the stairs). You’re asserting a control of his environment and that can be frustrating for him.
To this end, I would say you have a decision to make. “Give in” and return the stair territory and give him more upstairs space, or work through reinforcing that he cannot pee and poop outside that litterbox. I ended up letting Wick have access to the office occasionally to satiate his need.
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.