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Yopur babies are NOT as good as dead when you put them in the coop. And it is not too late to start medication if that is your desire. By the way, from reading a lot of posts, I think Silkiechicken and SpeckeldHen are two of the gurus of cooci on this forum. Personal opinion and I'm sure I'm slighting others, but these two are good.
As has been pointed out, most medicated feed contains amprolium. This is not an antibiotic. It will not cure anything. It reduces the reproduction of the protazoa that causes cocci in the intestines of the chicken. When chicks first ingest the cocci protazoa, they start to develop an imunity to it. There are 6 or 7 different strains of he protazoa that causes cocci. If they develop an immunity to one, they do not automatically have an immunity to all of them. They have to develop that immunity separately.
Small concentrations of cocci in the intestimes are normally not a problem, although I suspect (don't know, just suspect) that some strains are stronger than others. It's when the concentration gets high that problems develop. If concentrations get high enough, they can kill a chick. The medicated feed with amprolium allows this immunity to develop while limiting the amount of the protazoa that reproduces in the intestines, thus reducing the concentration.
Concentrations can get very high in the litter, especially if it gets wet. Even with the medicated feed, the chicks can get enough cocci protazoa by eating the poop that they can get very sick. That's why it is important to keep the litter dry and regularly clean out the brooder. If the litter is dry, most people seem to find once a week is sufficient, but kind of go by smell too.
As I said, there are several different strains of the cocci protazoa. You don't know which your chicks have been exposed to or which they have an imunity to. If you have an existing flock that goes outside, I guarantee you that they have some cocci protazoa. Don't stress too much as people successfully introduce brooder raised chickens all the time to their flock, whether raised on medicated or unmedicated feed. It is possible that, when the chicks get to go on the ground the existing flock has been on that they will pick up a cocci strain that they do not have an immunity to. They can also be exposed to internal or external parasites or diseases that are in your flock. The risk level goes up. It is not a time to freak out or panic, but a time to observe.
Hope this helps some.