How long has the rooster been gone? You should expect it to take some time for everyone to adjust. I have had some that just prefer to hide, I just let them do so and I will make sure they get something to eat and drink too, some aren't cut out for the drama. Many times after even months of hiding they will emerge one day, having found some confidence. I'm assuming since you hen can sit on the roof your set up is smaller, which can make it hard for all the members to feel comfortable, the bottom birds need to stay away from the dominant members or risk constant punishment, if the set up is smaller they can't always get away.
They are mingling together well and no one is chasing any more.