Here's the problem in a nutshell - it begins with a hen with low self confidence and the flock picks up on it, turning their focus on her. It's one of those self-fulfilling conflicts where the fear of the individual brings about the very thing she fears.
I had a hen like that a few years back and I tried saddles on her, that greasy, yucky Pick-no-mor, and separating her. I was at a loss. So I just left her in a pen adjacent to the flock during the day, returning her to the coop to roost at night with the others.
Well, guess what happened. She was gaining self confidence during the time she was in a safe enclosure during the day. I didn't know this until, after six weeks of confinement, I let her back in with the others. I was astounded when she stood up to the challenges that accompany a bird returning to the pecking order. She had gone through a personality change!
Since then, through somewhat obsessive observation, I've learned that self confidence plays a huge role in the behavior of individuals and the flock's reaction to those individuals. Introducing a new adult chicken to the flock is a case in point.
Recently I rescued a hen who had lost all her flock. She had been top of the pecking order, but coming to a new flock, she was forced to the bottom. I had her in a safe pen adjacent to the flock during the day, and over the next few weeks, I would force her to spend increasing amounts of time with the flock, enduring the pecking order. At first, she would spend just a few minutes at a time getting pecked and bullied, and the majority of the time in her safe pen, growing self confidence.
After two weeks of increasing time in the pecking order, she finally quit being afraid of the others, and that was the key factor in her being accepted by the flock. She is now relaxed around the others, and only occasionally does a flock member pull rank on her. She's settled in nicely and no one is focusing on her.
The thing you need to do is to create a safe pen for your bullied hen. It needs to be large enough to be comfortable with food and water. She will still be in the flock's proximity and won't lose her rank by being separated, which makes it all the tougher when you bring her back.
She will have time to heal and grow back feathers, and best of all, she gets to rest and recover her self confidence. Let her roost at night with the others, though. This is very important. She must not be seen by the flock to have left them. In time, let her have a few minutes at a time in with the flock, then put her back when you see the stress getting too much. Increase the time each day, but let her have the majority of her day to rest and get her mojo back.
You'll begin to see a big difference in her behavior after three or four weeks, and you'll see that the flock won't pick on her as much, either.