I’m not sure what your question actually is. Next time a hen goes broody and you want her to hatch chicks, I suggest you gather all the eggs you want her to hatch and start them at the same time. Mark those eggs so you can tell which ones belong and check under the hen every day after the others have laid for the day. Remove any that don’t belong. As long as you do that every day, you can use them without finding any surprises inside.
One of the bad things that can happen if a hen gets more eggs than she can cover is an egg gets pushed out from under her and cools off and dies. Eventually it gets pushed back under her and another gets pushed out and dies. If a hen has more eggs than she can cover you usually don’t get a very good hatch.
You have an unscheduled staggered hatch. It takes about 21 days of development for an egg to hatch. When eggs start at different times, some hatch long before others are ready. If it happens under a broody, she will stay on the nest for a while, but eventually she needs to take the chicks that have hatched off to get food and water, leaving the rest to die. In an incubator, you don’t know how to control humidity or turning. Those are really stressful. I feel for you.
Mark the eggs that are under the broodies and stop that hen from adding any more by checking under them daily. When they hatch and abandon the nest, move any eggs that are left to the incubator and keep plugging away along with the ones you already moved. You’ll probably get some more chicks. If any hatch about the same time as the chicks under the broody, you can give them to the broodies to raise, but you’ll probably have to raise some of them yourself. It’s a mess but just do the best you can with the situation in front of you. It’s all you can do. Good luck!
