Most of the time, excessive bullying and territorial behavior is caused by too little space. Anytime you remove a flock member, even for a short period of time, it changes the flock's social dynamic. Reintroductions are always a challenge when dealing with adult birds, with mature roosters it's even more so. They need lots of space, more the average 4 sq ft of coop and 10 sq ft of run, to help reduce territorial tensions. And reintroductions need to be gradual. This is where a small grow-out coop comes in handy. You let the bird needing reintroduction live next to the flock, but the others can't bully. They get used to having him around again and then you start to let them have free-range time together. Then, when everything is smooth during the ranging time, you can let him live with the main flock again.
Unless you have about 10 hens per rooster, I suggest you setup a bachelor coop and run for the boys. Without any hens living with them, they don't really have much to fight over.