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If the medication in the feed is amprolium, it doesn't inhibit it's immune system form working. All amprloium does is inhibit the growth of cocci by blocking thiamine. It is a thiamine analog. This allows the chicks who get exposed to cocci, you want to expose them to your soil early, to become immune to it at low levels, with a lesser risk of getting sick from cocci.
In other words, the usual medicated feed just prevents cocci from reproducing, allowing chicks to become immune without getting sick.
That said, if the chicks are not exposed to the soil, while they are on the medicated feed, they cannot gain immunity, and the med has no point. It is only effective if exposed at low levels. If soil concentrations of cocci are so high they can eat a dose high enough to make them sick, the meds also do nothing, as it's sole purpose is to inhibit the growth of the cocci protozoa in the gut.