"I can see where these two conditions occur naturally and obviously it happens, but are there any examples of where current bee breeding has fixed an allele, beneficial or otherwise, in the current population?  "


How about cordovan as one example?  Here you have a color gene that by itself provides exactly zero benefit to the commercial bee and probably some mild negative benefit in the wild.  Yet it is well fixed in some populations and sought after by some people.  In truth there are likely lots and lots of examples.  But assigning a specific allele to things like honey production, low swarming tendency or gentle temper is very hard to do in practice as those things all involve multiple alleles and we simply do not have total sequences for a few thousand honey bees to provide a data base to mine.

Dick

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