You should get the already hatched ones out of the incubator. Typically when you are going to do a staggerred hatch. You incubate in one device and hatch in another. For example. My incubator has been going since January with eggs revolving in and out. My hatcher takes a batch, they hatch, then I clean and disinfect the hatcher and get it ready for the next batch to hatch. The issue is that the live chicks may start pooping on your eggs or role them around too much. The live chicks can also introduce bacteria via the egg of the unborn.
Don't freak out, your unborn eggs are not 100% dooomed. Just take precaustions and get the lives critters out and try to keep the unhatched eggs in a clean environment.
