I do think limiting their space temporarily is needed – even if it is hard to do. It is much harder for a rabbit to understand where they should go to the bathroom if they have free range of a large space. Limiting the space and slowly increasing it as they progress with their litter habits is the best way to solidify good, long-term habits.

You said every time you remove a litter box they go the bathroom there. Is it the same box every time or any box that you move? If it is the same one, keep that box in place and try removing other ones. Do they have a stronger preference to use one box more than the others? Noticing which boxes they use more often may help.

Soak up any urine accidents with paper towel and put those in the boxes, too, along with any stray poops. The smell may help them figure out where to go. Use white vinegar to clean up old urine spots so they won’t be confused and have accidents there again.

I think limiting their space will help keep your carpets from being ruined with stains, too. If you have an x-pen, use it to make their space bigger and bigger every few days. A little at a time until they start understanding where to go (and not go).

Can you tell which rabbit is causing more accidents? That may help to know. It could be territorial. Are they fully bonded, and if so, how long have they been bonded? There could be some residual hormonal action or claiming space.