You mark the eggs so you know what you set. Hens will climb into her box and add eggs to her clutch (or she'll steal them from the neighboring nest box), then you get a mess of eggs that are at different stages of development. So if they are marked, then you just check under her and remove any unmarked eggs.
ETA: When you have eggs that are at different stages of development, say several days apart, the first chicks hatch, but the others haven't. So after a couple days, the hen has to decide whether to get off the nest to care for the babies (and let the eggs die) or stay on the eggs (and let the chicks die).
ETA: When you have eggs that are at different stages of development, say several days apart, the first chicks hatch, but the others haven't. So after a couple days, the hen has to decide whether to get off the nest to care for the babies (and let the eggs die) or stay on the eggs (and let the chicks die).
