Well, where are you located? It's fall here, and molting season, time for feathers to fall out naturally. Each bird experiences their molt differently, so your one bird could just be molting before the others. And a lot of chickens in their first or second year only experience a partial molt.
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My normally beautiful EE and her worst molt ever a couple weeks ago!
Pecking order differences and some squabbling are completely normal amongst a healthy flock. Birds at the top of the order are just asserting their leadership. Unless you're absolutely sure that one of your birds is intentionally feather-picking and it's becoming an obsession, or there's blood being drawn, I don't think you have anything to worry about, truly! My biggest concern would be integrating ASAP.
Do you plan on keeping them separate? Unless you need separate pens for breeding purposes or for a broody hatching her own clutch, it really is much easier to manage your birds as one large flock all together. You may be stressing for no reason and creating more problems for yourself. Chickens are flock animals and will sort it all out themselves. You may find that one of your roos will turn out to be an excellent flock protector and also show the ladies where to find the best snacks.
Yes, quite possibly...
It sounds like you might have too many houses for them to choose from, that can get really confusing for them, especially if you plan on adding another one and moving them again later. One big house for all the birds would make them happiest. They naturally want to follow their leader and go where the leader goes, even though they don't necessarily hang out shoulder to shoulder. If you have 5 older birds and 5 new ones, you need ONE coop big enough to hold 10 birds with at least 10-15 feet of linear roost space (bars) for them to sleep on. You would be fine with only 2 or 3 nest boxes to lay eggs in.
Here's another article that may clarify what I'm talking about:
How Much Room Do Chickens Need