I'm sorry to hear of your troubles. It's best not to let any of them fly when they have eggs or babies (but maybe your hen escaped on accident). You can pretty easily order vaccines for them and do it yourself, which cuts down on deaths and illnesses by a HUGE amount (I speak from personal experience!). A lot of times when it is the babies dying, it could be paratyphoid as this kills the young and older birds first. I hope things smooth out for you.