A lot of posts here talk about how rabbits act generally, but it’s always important to think of each as individual too, so I’ll share how I navigated this with Wick.
Wick has a hutch and he too made a huge mess of it. My goodness, poo and pee everywhere! I had a pen set-up in another room, so I would move him there while I cleaned the hutch, so Wick had two “homes”: 1) Hutch and 2) Pen. While he wasn’t in one, I’d clean the other.
Cleaning it will remove some of his scent, so to help transfer the scent back into a clean hutch, I recommend putting a blanket or fabric down in the hutch that you can remove when cleaning, then replace afterwards, so the hutch doesn’t smell entirely Eeyore-free when he re-enters!
Now speaking generally, a lot of rabbits don’t like their place being cleaned while they’re in it, especially when I bond isn’t fully built yet. The rabbit can get defensive or scared, so I recommend relocating Eeyore while you clean (i.e. pen). The pen will also be helpful for litter box training! Training in a hutch is hard because you can’t observe all sides of the environment, and it’s difficult to move the rabbit into the litter box after an accident occurs. In a pen, you have that freedom of observation and motion so training sessions are more effective.
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.