Yes, the feathers will most likely grow back. My friend had a hen thats whole body (almost) was feather picked and she put ointment on it daily. Now she has all of her feathers back, and she was worse than your hen.
You can rub some REGULAR Neosporin on her rough areas or even Vaseline. Blu-Kote would also work quite well and to prevent this from getting any worse, you could buy or make a "chicken saddle".