It's all good. It can get confusing when dealing with a broody mom, her rank in the flock, the other flock members and their ranks AND the moms hormones telling her to be fierce....or not.
There are a lot of variables within each flock.
It sounds like your birds have been together during the...
You want them in there while mom is still protecting them. I would do it now. If you wait much longer mom won't protect them....part of moms job is integrating the kids into the flock.