If the spot isn’t too big, you can spot clean with water and vinegar and just re-arrange things slightly so it can air dry without the litter box over it. Workflow wise, you can probably that the fleece off without needing to deconstruct the Xpen, but just strategically lifting it section by section by section as you gather the fleece? For the future, if he is not a fabric chewer and this may be a “high risk” area, you can purchase a water proof diaper pad or something to put on top, that way it’s not a huge operation to clean the entire floor, especially when only a spot is soiled.
At these times, it can also be helpful to have a back-up floor covering, so the rabbit doesn’t need to wait for an entire wash and dry cycle. He could maybe wait in a carrier while you take off the old fleece and put on a new one.
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.