I think that underlying this thread and possibly any discussion of the breeding of bees, are some serious misconceptions. What characterizes a geographically distinct population? For example, what is it about the Carniolan Race that makes them distinct from any other? How did such a thing as a race of bees come about? 

Obviously, this population was isolated from other populations, such as Apis mellifera mellifera, for a very long time. And in the region where they exist, they were subjected to different selective pressures than the bees of northwestern Europe. We don't know what these factors were, maybe diseases or predators, maybe climate or floral composition -- selective pressures sculpted these populations by eliminating individuals that could not survive to produce progeny and whatever weaknesses they expressed dropped out of the gene pool. 

However, this does not mean that the resultant pool is not variable within very wide parameters. To us, it may appear distinct from say, the bees of Madagascar, but one would expect within such a population there would be wide variability. Variability is crucial to the success of a given population, since it produces individuals that are unlike there mates in many ways. 

If heterosis leads to robust progeny then there is strong pressure to maintain wide variation in a population, whereas if inbreeding leads to weakness, those individuals that have a propensity to inbreed, will tend to drop out of the population as a result of producing inviable offspring. 

What I am saying is that one must view a large population and analyze what makes that population successful as a whole. Many features of the honey bees' mating system seemed to have led away from inbreeding, presumably due to the harmfulness that it causes them. We know that if a queen mates with a drone that is too closely related to her, she will produce diploid drones due to being homozygous for the sex allele. 

Conversely, colonies that are a composite of many diverse patrilines seem to be much more vigorous, so that over time the trait of "not mating with other bees that are related to you" would tend to be enhanced in a given population. This could lead to many unrelated families, all expressing this trait, due to its enhancing their ability to survive. 

But then, you take a lineage out of this population and attempt to propagate it, and you have isolated it from the very conditions that led to the production of this trait. One would rightfully expect this trait to fade if you began to develop a line and these bees crossed with one another.

We all know that human attempts at using breeding to produce uniform results can have catastrophic consequences. Look at the tragic weaknesses in our various breeds of livestock, pets, etc. Why would bees be excepted from the rule that if you ruthlessly select for one or two traits, you end up with a product that may be non-viable and require extensive life support?

Breeding via selection without fully understanding the consequences, is just as foolish as using chemical controls willy nilly. The result may be a far cry from what you were after. Like the antibiotic resistant "superbugs", for example.

PLB

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