Can you put the nursery coop(does it have a run too?) into the main run?The Mom and chicks lived in a nursery away from the flock that's why they are separated.
Our flock lives in a 45' by 45' yard and there is one main feeder, there are not many hiding spots we have a coop and two shelters, very open. Yes, we have had some injuries one of the chicks has 2 pretty good sized pecking wounds on the vent ( caused by mom).
Clutter up that run! Put out multiple feed and water stations.
Here's my run during chick integration time:

