At this stage,they really don't need protecting. They will figure out their rank in the social order on their own. You could have had them integrated by now if you had allowed the broody hen to introduce them as small chicks to the flock. Being over protective of chicks until they are half grown doesn't help them.
How "separated" have they been? Out of sight? In an enclosure in view of the flock all this time? If the first, you will need to introduce them as you would strange new comers - see but don't touch barricade until the flock becomes acquainted with them and they become familiar with the flock.
I the chicks have grown up in view of the flock, just turn them loose in the run now. They'll figure things out since they will already be familiar with the adults.
Two different choices according to how familiar the chicks and the flock already are with one another.