Behavior will tell you if your chicks are sick or well.
Well chicks eat, poop, race around all day, and sleep only occasionally, then sleep all night.
Sick chicks are droopy, sleep a lot, and are lethargic. If you look at their eyes, they are often red-rimmed and droopy lidded. They may have a discharge from their eyes and nares. Lung problems will sound like plastic crackling when they breathe.
Poop of well chicks is firm, except for cecals which should be the consistency of chocolate pudding. Sick chicks have runny, watery poop, and sometimes brown diarrhea. If there is any blood in the poop, suspect coccidiosis. Chicks will behave sick, and Corid is the treatment. It's not uncommon for chicks to get it, especially since you had a bout of wet bedding and it may have allowed cocci parasites to multiply.