Does your pop door open up into a predator safe/mostly predator safe run?
What I'd do is this: close up the chick coop so they can't use it, and encourage them to follow the adults into that coop. If they don't want to go in, manually put them in (as I integrate when chicks are younger, I actually put them in a cage inside the coop for a few nights before progressing to next stage.)
If you have an auto door, disable it or prop it open. This way the chicks can hightail it out of there if needed once daylight comes. Do this for a few days (3-5 days for me) and if everyone seems to be doing fine, you can go back to closing up at night.