Question? you are not adding salt to the tank i hope. Cories do not tolerate the salt.
Corydoras are also very dosile and sometimes fall the victim of aggression. They tend to preffer the company of other corydoras IME they do better with a friend / partner.
It does sound like a secondary infection if the gill area is discolored or redish. The chances it was caused by the debris is slim to non. Now, there is a poss. that it picked up some nasty stuff and it caused and infection. But I doubt something got stuck in his / her gills or gill plates.
If there is or was an amonia spike this would cause the discoloration and behavior. I have had corydoras in the past that out of the blue have come down with swim bladder problems. And in most cases that is or can be caused by a foul tank. In this case a tank that got foul while cleaning. Just a thought.
I would suggest not trying to move him at this time because anymore stress may do him in. But, do suggest getting him away from the rest till he recovers or till you can determine who if any fish is picking on him.
Hope this helps. As we speak i am looking through to see what it may be or what may have caused it. book #1, book #2 will keep trying.
Danny