To try to get back to HP's initial thread idea. I know very little about bees, as I am a complete newcomer, but am enthusiastiic to learn, and am finding this forum tremendously useful. However because of my work I do know a lot about disease.
I would draw a parallel with TB and smallpox in this country. At one time TB was virtually eradicated through better nutrition and living standards ( good food and accomodation), social hygiene - " no spitting in public places" ( I remember those signs on the buses when I was a lad)( good apiary hygiene and practices), antibiotics, and vaccination. However as immigration has increased, and poverty returned in some areas the disease has returned and is now again quite common, and is much more resistant to treatment!!
Take smallpox, it was eradicated in this country, until it escaped from a research lab in Birmingham about 20 years ago. Mercifuly through tremendous effort the outbreak was contained and eradicated.
We are animals, bees are animals. The same rules apply. It takes a long time to eradicate disease totally, which brings problems of it own ( like resistance), and the approach is always multi pronged, then it can so easily re-appear. Sometimes we just have to live with disease and minimise the damage it does. First the disease needs to be understood, and there seems to be large gaps in knowledge about bee diseases.
As to breeding, that would take some time to be effective , unless one went down the GM route!!! ( enough said).
Sorry if you find this irrelevant, but it is just my take on a fascinating thread.