Firstly the cleaning while you eradicate the bacteria chlaymydia, and any virus , pain in the but it may be, us a must. As is replacing the breeder box's as I don't think they can be properly cleaned. Over time the best box is going to asotb birth fluids, regurgitation, and waste, which provides breeding grounds for nasties.
Second , chlaymydia causes liver enlargement. Acutely or chronic. There are links with chronic inflammation and cancer. Just like there are links with virus and cancer, and genetics, and environmental toxins. Life is complex, and individual response to disease varies. You could have multiple things goin on in your flock, and in individuals in the flock.
This paragraph I found talks about liver inflammation and enlargement with chlaymydia.
"This is from a difference article
Budgerigars (Budgies)
Budgerigars, or budgies, commonly develop cancerous tumors in their kidneys and reproductive organs. Kidney, ovarian, and testicular tumors often cause a unilateral (one-sided) lameness that owners often mistake for an injured leg.
Goiter (underactive thyroid gland, or hypothyroidism) also can occur in budgies, especially when they are on all-seed diets. Seed contains very low levels of iodine that is required by the thyroid gland to function properly; therefore, the gland swells to try to extract all the iron it can from the seeds. Budgies afflicted with this condition are often overweight and have a squeaky voice or regurgitate when they eat as a result of the enlarged thyroid gland pressing on the esophagus.
Another condition commonly seen in budgies, especially when they are in close contact with other budgies in pet stores, is psittacosis (also called chlamydiosis or parrot fever). It may be carried by budgies without them showing any clinical signs, or infected birds may show respiratory signs (sneezing, difficulty breathing, decreased ability to fly, and tail bobbing) or a swollen abdomen from liver enlargement.
Since many owners incorrectly feed all-seed, high-fat diets to their budgies, obesity is common in these birds. Hepatic lipidosis (fatty liver disease) is a problem that often results and causes death. This species also is predisposed to poor diet-related (high-fat, all-seed) tumors called lipomas and xanthomas that may be found on the wings and ventral abdomen. Lipomas appear as pockets of soft, white, moveable fat, while xanthomas are typically firm, fixed, and yellow-orange.
Reproductive problems are very common in pet birds, as well. Egg binding is seen often in pet budgerigars, even those housed individually without a mate, that are still capable of laying eggs. Birds often become egg bound when they are eating diets high in seed that lack calcium and vitamin D, which are critical in the formation and laying of eggs."
I'm not the best at understanding genetics. But I've worked with endagered species, and it's generally regaurded that you need 100 individuals at a minimum in a wild population to insure genetic diversity. So depending on how long this breeder with sixty birds has been breeding, and wether or not new stock is aded , there could be loss of diversity. But when selecting for color mutation it's always a good idea to add normal color stock back to the program. As I understand it from reading about a well known lutino Quaker breeder. As when you are selecting for color, there are other genitic factors that are linked. You can't really just select the color factor of genes, other traits are linked. As again in Quakers the blue quakers are smaller than other color quakers, so somewhere along theine color was linked with size, and color mutations are back bred to establish the color..
We have a few avairy breeders here. Perhaps you can start a new thread asking for their cleaning practice, if they do replace nestboxs at certain intervals. How they manage diseases outbreaks and loss. I fear I'm nearing the end of my usefulness to your issues. But your frank discussion of your Budgie loss, will no doubt be helpful to others.
