Some good advice above!
Just to re-iterate, go ahead a touch the babies!! Put your hand in the nest and feel around. It is very important to remove any dead babies or left over placentas otherwise they will go rotten and make the other babies sick.
Did she pull fur and put that in her nest? Some does will build nests for up to two weeks before giving birth, but most only pull fur right before giving birth.
Good job seperating the buns. It's not really a matter of the male killing the babies, it's the fact that he can (and will) make the girl pregnant again immediatly after she gave birth. Which is hard on her and her babies as she will lose her milk as the second litter comes close to being born. Not to mention you will then need to find homes for two litters!
So, go look in the nest, take pictures if you can, and tell us if there is fur and babies in it.
If there are babies, they should have round looking bellies(like they swallowed a ping pong ball). That means mom has fed them. Mom will only feed 1-2 times a day and she will jump on the nest, move the fur aside and stand over them while they nurse from beneath. You probably won't see her feed them, so just check them for round bellies to make sure they are being fed.
It would be a good idea to look into getting the boy neutered now, as by the time mom is done weaning the babies you can get her spayed then re-bond her with her boyfriend.
I would also recommend finding a vet to sex your buns just to make sure you do have a boy and a girl.
Good luck, and please ask as many questions as you need. We are here to help!
--Dawn