I left my momma hen and her chicks in the run, seperated for a couple days with 1 inch chicken wire. but new baby chicks can fit thru 1 inch chicken wire. I kept her on the other side for about a week then removed it. there is a ramp to the nest box, baby chicks went up and down the ramp no problem although I did have one that needed to be shown the way a time or two.
Other hens, most mommas will thrash any who get to close but sometimes they are looking the other way. I had a pullet who was intent on pecking the chicks even while they were under their mom. I removed her to chicken jail for a week. When I tossed her back in she was low on the pole and they all picked on her. ended the chick pecking problem.