How old are your roosters? Are they both mature or still cockerels? How big in feet or meters is your large fenced in run? It sounds like they have feather loss but what do your overused hens look like?
If the feather shaft is totally gone the feathers should grow back before too long. If part of the shaft is still in there they will not grow new feathers until they molt.
It’s fairly normal when you have two mature roosters in the flock that they split the flock, each with his own harem. The set up separate territories so they don’t have to interact. It sounds like your coop/run set-up may not be big enough to allow that. Small space often increases behavioral problems, for roosters as well as hens.
Why do you want two roosters? If one is causing the problem why not get rid of him? We all have our own goals and reasons, I don’t know if this is a potential solution or not.
Have you checked for mites and lice? They can cause feather loss.
Have you seen something other than feather loss that makes you think one is overly aggressive to the hens? If so, what? I remove overly aggressive chickens, male and female, from my flock. There are too many good ones out there for me to put up with a bad one.
I’ve had problems in the past where certain hens have brittle feathers. If it’s flock wide you may have a nutrient deficiency but mine was genetic. The hens did not process the nutrients require to make the feathers supple so no matter how gentle the rooster was they lost feathers. When I removed those hens and reduced the hen to rooster ratio the problem went away and did not recur in future generations.
I’ve had a lot more problems with immature cockerels and pullets than mature roosters and hens. That’s why I asked about their age.
When I have a problem in my flock I try to determine if it is a flock wide problem on an individual chicken problem before I react. If it is a flock wide problem then I try to address the entire flock. If it is an individual or certain individuals I try to address them. I’m not totally sure what is going on with yours.
Often if you have a chicken misbehaving, male or female, isolating that chicken from the rest of the flock for a week or so cause them to change their behavior. It doesn’t always work but I’ve found it to often be effective. If your problem really is an overly aggressive rooster you could try to isolate him and see what happens when you turn him loose with the flock. The odds are pretty high the two roosters will fight when they come together, but they may be able to work out an accommodation. I’m not really strong on trying this, I think you are taking a chance with the roosters fighting, but it might work.
Keeping two flocks permanently separated may be a solution. You might need to enlarge or reconfigure your run, but keep the two roosters permanently separated with their own harem. I don’t know your goals or why you have the two roosters so this may not work for you but it has its merits.
This is a stretch but if the five hens are the problem, you could try isolating them, either short term or permanently. I really don’t like this one but if it solves your problem it solves your problem.
If the males are still cockerels, they have not yet developed a good technique for mating. Barebacked hens is often more of a problem with cockerels than mature males. Sometimes if you blunt the tips of the claws so they are not sharp you greatly reduce the damage. I’ve used a Dremel tool for that but there are other techniques. If you just blunt the sharp tip you are unlikely to hit the quick, but it’s still a good idea to have some flour on hand to use to stop the bleeding if you get too deep. Even if you do get too deep and get some blood it doesn’t permanently harm them, but I don’t like to see blood any more than anyone else. Some people talk a lot about spurs doing damage but on cockerels the spurs are usually not big enough to be a threat. On adult roosters blunting the end of the spurs can be useful though.
That’s about it. Try to identify your problem and treat the causes. If it turns out to be specific chickens that are causing the problem, get rid of them or isolate them so they don’t cause a problem. If it’s lack of space try to give them more space or reduce your flock numbers.
To your questions on your second post. It’s hard to say how long you need to keep them in the second coop/run before they make a permanent switch if you later give them the option. I often go from two separate coops into one, just moving them into the main coop after they settle in for the night and locking them out of the second coop. It usually only takes moving them into the main coop once or twice.
I’ve gone the other way a few times. Usually a week is enough for them to start using the second coop but occasionally I have to separate them and lock them up again. On rare occasions one chicken in ether coop may spontaneously decide to switch. You are dealing with living animals, about anything can happen. There can be a lot of trial and error involved.
A lot of people deal with these issues by creating a bachelor pad. They keep the males separated from the females so there are no females to fight over. They will still establish a pecking order but usually bachelor pads work pretty well. I’ve done that with cockerels where the pullets hung around just outside the bachelor pad and it was really peaceful. Some people say they have to put the bachelor pad totally out of sight of the females for it to work. You are dealing with living animals, often there are no clear cut answers.
How long do they need to be isolated? How old are they, how close to maturity? Are they the real cause for the problem? You may just need to isolate them until they mature. You may need to keep one locked up forever while letting another back with the hens.
