Do they have a cage you could confine them to while you litter train them, so they learn to go only in the litterbox? 

That’s what I did with Ivy, and she’s never had a problem, she even always poops in her litterbox 

Have you tried containing them to just a cage area until they are better with their habits? Sometimes bunnies need to be confined for a week or so until they can remember exactly where they’re supposed to go. If you let them continue free roaming, I think they’ll continue to pee because they’ve learned that the carpet is fair game.

Also, before you let them out again, make sure you clean the carpet very very well with a vinegar and water solution – if they can smell pee anywhere, they’ll continue to mark. I would even think about renting a carpet steamer and doing a really good clean.

Sometimes soft absorbent things are just too tempting to bunnies, but you can’t exactly get rid of your carpet, so I’d try confinement for a while plus deep cleaning and see if it helps.

Be sure to use large litter pans – it’s possible that they are too confined and they miss, or they don’t like sharing a soiled spot with each other and are peeing over the side to avoid it. It also could be a protest against a type of litter they don’t particularly like. Bunnies tend to misbehave to try to tell you something, and when you fix it and they approve, they behave better. Maybe get a large litter pan and a small amount of a different brand/type of litter, and add it. See how they respond. If you use wood stove pellets, try something soft like carefresh. If you use soft, like that already, try Aspen pellets or a small bag of Feline Pine.

You can buy screens for the litter box (BB sells some) that will keep her from digging the litter out. If she’s only peeing outside of the ones she’s digging at, then that might be the connection.

Hopefully the screens help solve the problem. Have you tried taking out the ones they llike to dig? Also, if those boxes are older, sometimes they can harbour the pee smell. So somebunny might be telling you this is not acceptable.

Can you put them in a pen with a solid floor, linoleum or tile? It’s possible that they don’t distinguish the carpet being different from litter.

That should work. Just something that can be wiped down and disinfected should they pee on it.

So that’s about 2.5 by 5 feet? That’s small for two rabbits, even short-term. Can you set a pen up in the kitchen or somewhere with solid flooring?

Yeah, maybe put down some cardboard. That should work. I wouldn’t go any smaller than 4×4 feet. Keep them confined for a couple weeks with limited supervised time out. You need to pretty much start over with the littertraining.

The box house should be ok to add. Provided it doesn’t cause any fighting. Sometimes when rabbits are confined more than the norm they can have little tiffs over items or space.

You could use their c&c cage to confine them if a pen is not an option.