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As I've often said, size isn't important, it's the spirit of the rooster. It's not that unusual for the smaller one to be the dominant one. And thanks for the information that they got along for two years before starting fighting. That's good info.
My guess is that when they were free ranging they each had their own territory, but when you locked them together they had to share territory. The serious fighting started. It sounds like they are still locked in the run so they cannot go back to their established territories.
If you can turn them loose so they can get back to their territories the fighting may stop. But until then I'd try housing them separately so they can't fight.
Thank you. Yes I believe that's the main problem. They haven't been free ranging daily like they were before, I just let them out less because I've been losing them to predators recently. They're safe with my 3 large dogs as long as they stay inside the fenced part of the yard where they are, but of course you know they love to roam. My dogs still alert me when they hear a disturbance in the flock but they're confined and can't do anything about it. I would leave the gate open so my dogs could stay with them and protect the, but I have a neighbor with an aggressive Pit Bull that tends to come on my property often. It's very annoying because it's always picking fights with my dogs even through the fence. I'm going to give them a separate living space but still let both flocks free range, and hopefully they'll stay out of each others way then.