Leaving the does together may make it difficult knowing which babies came from which doe. You could wait until a doe is showing before giving her a separate tank. I think they'd be all right; just give them stuff to build a nest ball and a little new stuff each day; that'll keep the doe occupied and help her instincts kick in. Usually does who litter together get along just fine but on occasion if one litters days before the others there can be jealousy resulting in mousenapping, which is hard on the babies. I'd just keep a close eye on the does when they are nearing their delivery so you can intervene if necessary. Removing a doe and her new babies to a fresh tank, or the ones still pregnant, shouldn't be a problem either. I'd watch out for your fingies, though, as the new and expectant moms can get nippish.