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No, you're missing an important point. When they get sick they're not allowed to "recover or die", they're culled. Even if they were to recover they'd still be genetically predisposed to the particular disease. Obviously other birds in the flock would also have been exposed to the particular pathogen. The ones that don't get sick are the ones you keep to breed from.
So then, how did the ones that didn't get sick from exposure, get that way? From parents that survived the preivous sickness, & passed on it's surviable genese, the ones that died, can't! Again, if you cull the ones that ARE sick, & you don't give them a chance to recover, yer just artificially selecting bad genes...lets say, 9 outta 10 that you would've culled, died, & only one survive, if you allow that one to breed, from another survivor group & the same sickness exposes to it's progeny, you'll probably have 3 outta 10 survive & then their offspring will have more capable immune system to produce a more roubust progeny.
A bird that has resistance to disease may have a strong immune system from good genes or great nutrition. A bird that survives an infection is just lucky. I don't know if antibodies can be passed to the egg, but some infections can.
Dale-Ann