Unfortunately, the issue is the way you are trying to breed your birds. It’s never a good idea to try to breed birds in a colony like you are doing. When you breed most species of birds in captivity, you need to only have one pair of birds per cage. It doesn’t matter how large your aviary is, when you try to breed birds in a colony or group, you will never have a high success rate and you will have a lot of health issues with the birds. There are breeders who breed this way for profit, because making money is their main goal. But they end up selling weak, inferior birds. A serious breeder would never breed birds in an aviary. You have no control over which males mate with which females. You end up with a few dominant males that breed with multiple females, which results in most of the offspring being related, and a very weak gene pool. Birds will fight and raid each other’s nests, destroying eggs to lay their own, or killing chicks. If you fail to remove all of the offspring and leave any in the aviary to breed, they end up breeding with their parents, brother or sister, cousins, etc. and then the gene pool gets even weaker and the offspring even more inferior. When disease gets introduced into the colony, it is very hard to treat and control, because every single bird has to be treated. I don’t know what disease or organism your birds have, but you need to have them diagnosed by an avian vet, and then you have to medicate every single bird. I would recommend that you take down all of the nests, and take some of the sick birds to a Vet to try to find out what is wrong with them. Once you have treated all of the birds, I would not recommend any more breeding. Enjoy the birds, but don’t let them build nests and discard any eggs you may find. I can’t give you any different advice, because if you continue breeding like this, more birds will suffer and die. If you are trying to breed birds to sell, then I recommend that you get separate cages for each breeding pair. Your chicks will be healthier and stronger, and in the long run you will make more money.
Thank you for asking Lafeber,