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There is no need to separate them at this point, because if the rooster brought any respiratory diseases to your flock, they've already been exposed. Mycoplasma gallisepticum (MG) is a common respiratory disease that can cause swollen eyes, along with bubbles in the corners of the eyes...

Did you get your birds as day-old chicks from a feedstore or national hatchery, or from a private seller? Coryza has a very bad smell; if you sniff near their beak or nostrils, you should easily notice the odor of coryza.