I take the nestbox (with the babies in it) outand put it someplace warm and cozy and safe. I havea large plastic tub in my laundry room that I put the whole nestboxinto (incase someone tumbles out, they don't crawl away).It's warm in there.
Mother rabbits don't sit on their litters the way birds or otheranimals do. They feed twicea day, for maybe 5-7minutes... they have no interaction with the babies inbetween. And I've never had a mother refuse to nurse theirlitter when presented with the nestbox. THey hop right in...
At 21 days of age, (3 weeks old), I take the nestbox away. Ifind the babies tend to stay healthier, cause even if the momma isn'tpeeing in the nestbox, the babies might. And after 3 weeks ofage, it's a lot to ask the mom to clean up.
I only do this when there is a problem, like what you described...it's worked very well for me in the past....