Rudy's Roost,
Hello, neighbor! We're in Ashtabula County too and our flock is just under one year old. We started out with 2 cockerels, but only have 1 now for our flock of girls.
You said the hens that were just sitting in the nest boxes weren't laying any eggs. Were they laying eggs before? Did they raise their feathers and squawk at you when you approached the nest? They could have gone broody. Our broody girl gets picked on by the others in the flock. The girls don't lay eggs while they are broody. They don't need eggs in the nest, they even sit in an empty nest; but may move to another nest if she sees one with eggs.
Ella is right, any time the dynamics of the flock are changed (separation, increase or decrease of the flock, death), the flock has to redetermine the pecking order. This is normal behavior. Also, if a hen is using the nest box to hide, she could be lowest in the pecking order and may possibly be kept from the feed and water. I agree, make sure you have more than one feed and water area for the birds, so no one dies from dehydration or lack of food. If the hen is at the bottom of the pecking order, she will be under stress of being picked on by everyone else. A stressed hen does not lay eggs.
The wing shuffle and dance are aggressive signs. The rooster does that to remind the flock he is the head boy. He will also do this to another rooster before attacking. You have to be the flock leader. If you let your rooster attack you, he will see you as the weaker rooster. He may even try to fly at you and spur you in the leg or in the face. I've read that some people have had good luck holding and petting their rooster a bit each day while he is in isolation. This teaches him that you control him. Our boys have been very agressive with the girls in the past, but not with us. Unfortunately, some of our girls have feathers missing from the back of their necks from being pulled on so roughly. I've noticed that our boy always backs down from our alpha girl, which is funny because she is smaller than he.
I would keep an eye on the picked on bird. Make sure she has no injuries. If the others see she is injured, they may brutally attack her until she is dead. If she is injured, isolate her and treat her wounds. When one of our birds is injured, I try to let them spend a little time with the flock each day while I can watch them. This helps prevent them from gang attacking her when she is healed and returned on a full-time basis.
But, it is normal for the flock to peck at each other occasionally. If one bird is eating and another higher in the pecking order comes to the dish, she may peck at the first bird. It's as if she is saying, "Hey, I'm your superior, move out, I want to eat." I just try to make sure no one gets injured. You said you separated the hen that was chasing the bird you isolated. That is normal. I wouldn't separate them unless it got really brutal. They usually work out their pecking order problems pretty quickly.
Your flock doesn't need a rooster to lay eggs. But if you want to raise your own chicks, you either need a rooster or you need to purchase fertilized eggs. If you want the rooster for a breeding program, there are others on this board with experience in this who can answer any questions.
Good luck and keep us updated.
regards,
keljonma
if edited, probably for typos.....