You'll get different opinions on this so I'll add to the confusion. Here are a couple of threads that give other opinions. They might help you understand what is going on.
Number of roosters thread
https://www.backyardchickens.com/forum/viewtopic.php?id=219443
Managing multiple roosters
https://www.backyardchickens.com/forum/viewtopic.php?id=229968
I think what you are seeing is hormones kicking in and they are fighting to see which is the dominant rooster. It is not really a pecking order thing, though that factors in. It is about who gets the perks of being dominant but also what roles do they play in protecting the flock. If they can sort it out without killing each other, they have definite rolls to play in protecting the flock. For example, my dominant rooster is almost always the first out the pop door in the morning, going out to see if things are safe and take care of any problems. My second in charge is usually the last out the pop door, staying behind to protect the flock if necessary. Any below the top two just come out whenever they feel like it, mixed in with the hens. If necessary, they will fight to protect the flock and watch for predators, but they leave the main responsibility up to the top two.
I find that one of three things can happen when roosters fight. Sometimes one gets injured in any of these and that changes the outcome.
1 - They decide who is dominant and who is not. They form a good partnership to take care of the flock.
2 - Neither one is willing to take on the secondary position. Size is not important. They are so evenly matched in spirit that they wil fight to the death. I expect yours are like this, but when you removed the one, you knocked him down in the flock and he is not as comfortable fighting for dominance. Maybe something like you got him confused when you took him out and he is not sure what to do. I think it is very likely he will regain his confidence and they will go at it again.
3 - One rooster is so dominant that he just goes all out to kill the other. All roosters contribute genes to the continuation of the flock. The dominant one gets his choice but studies have shown that the ones that are not dominant also contribute a lot of genes. When one is so much stronger than the other, he tries to kill the weaker, as if saying "I don't want your weak genes in my flock!"
Multiple roosters can exist in the same flock and work well together. I see it in my flock all the time. But my advice is to keep as few roosters with your flock as you can and still meet your goals, because the more roosters you have the more likely you will have problems.
Good luck!
