He was probably tussling with other cockerels thus the rough feathers. Now that there is no competition for the top spot, he has to turn his attention to be hens and assert his superiority. Don't worry about only swapping out the one. They've only been with you for 2 days. There's no doubt that he is a cockerel so don't let him tell you he isn't. Pick a replacement that looks most like your pullets if you are unsure. He won't swap again.