Welcome t RabbitTalk, Summerdawn.
You can clean out the nest box any time it needs it. In fact, it's a good idea to do a through check of it even if the box looks clean, in case there should chance to be a dead kit underneath. It's usually best to take the box out while you clean it rather than working around the doe, who may become anxious. Give her a treat that takes a couple of minutes to eat, something like a piece of carrot is good.
Remove the box and transfer the kits to another container one by one. Look them over to make sure they are all healthy and that they are being fed. This will not bother the doe at all when you return them.
Save as much clean fur as you can. Dispose of dirty bedding and remake a nest with fresh materials. Replace the kits and cover them with the fur "blanket." Put the nest box back in the cage and you're done. If there is not enough clean fur, you can add some other natural material. Teased cotton batting, feathers from a pillow, excess fur you have saved from a doe that pulled more than was needed.
Edited to add: It is always a good idea to clean out the nest when the kits are 9 days old. It helps to prevent nest-bx eye if they have fresh bedding when their eyes open.
~ MaggieJ
