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I don't see anywhere that you mention your hen to rooster ratio; maybe you have too few hens for your number of roosters?
I'm a new chicken owner but I've owned horses for years, so I'll come at this from that perspective.
A) If I had a special needs horse like your hen Bobbles, I would be sure only to turn her out with other horses that were gentle with her and respected her.
B) If I had one or two horses that repeatedly beat up the other horses and did not want to sell them for some reason, then those one or two horses would be separated from the rest of the herd. Period. No exceptions. It is patently unfair for the animals that display good behaviour to be consistently punished by those who are bullies. Truth of the matter is that there are too many good horses out there to keep a bully, just like there are too many good roosters too keep a bully, but if you have to keep them then they need to be in their own pen for the safety and happiness of your hens and your good rooster.
C) Mean, aggressive stallions have a tendency to produce mean, aggressive offspring. I can only hypothesize that roosters are the same. Why would you want to continue that kind of bloodline? Your next set of chicks from your good rooster may produce some nice cockerels, but I doubt any chicks from your mean roos would be much better.