I am sorry to hear about your chickens been sick. I don't know basically anything about that disease. So excuse my stupid questions

but if it can't be passed from the head to the embryo in the egg then does that mean you can keep the ones that haven't hatched yet separate from the others and they will be fine? Will it run its course eventually and the ones that make it make it and then you can put all the surviving chickens and newest chicks together?
Your last sentence made me think that you are wanting to give up on chickens. I hope you don't. But I can understand how you would feel that way. This would be very devastating to me also.