So, you leave the mothers in the same tub as the others while she gives birth and then let her raise them in there also??
Oh, I've been putting the female or possibly two pregnant onces together in a separate tank to give birth and to raise their young - once the babies are weaned - I remove the moms and put them back into the female breeder tank again.
Yep, I just leave the established colony completely alone and take out the weaned mice as needed. If taking out the pregnant ones works for you, then there's nothing wrong with that. Although it might explain why she ate some babies if she was stressed by the move.