FortCluck
Hatch-a-Long Queen
I would give them some time to adjust because they were in such a big flock and now they are in a smaller one so they need to reestablish their pecking order. This can take up to a month from what I have experienced.They came from an over crowed flock of forty hens and a couple roosters.
Is the rooster actually causing physical damage to the hen or is he just pecking her and bothering her?