Ah. yes. Superfreak explained this several years ago, when some members were sure that it was due solely to contamination by wild flies, as genetic drift. Genetic drift is not an evolutionary process but a means of recovering from an evolutionary misstep.
In the case of flightless FFs, for example, a mutant gene supresses the full development of the wings. Normally, such a strain would die out almost immediately due to being outcompeted by flying flies, but under unusual conditions, the most common of which is selective breeding, you can obtain a "pure" recessive strain. The alleles for flight are still present, of course, but unexpressed. However, whether the trait is advantageous or not, the opposite allele will occasionally be expressed, and if conditions do not favor the mutant allele but the original, "dominant' one, then the population will drift back to its original phenotype. This is a particularly sad fact of raising "fancy" tropical fish such as guppies. Sooner or later, your lovely strain will "revert to type".
In a recent, hijack discussion on another thread, someone, Zephyr, as I remember, advanced a friend's theory that a new captive population of cockroaches, say, would be more resistant to disease, because after the first outbreak of disease, all of the survivors would have immunity which they would pass on to their offspring. Zephyr has made interesting comments and observations here for years, and I thoroughly enjoyed this idea; it ties in nicely with the research on an immune factor among humans who survived the plague. Alas, though, nature is not that obliging. Whatever diease, viral or bacterial, that afflicted our hypothetic roach colony, it was probably due to bad luck or bad husbandry, with an emphasis on the latter. Immunity would only be conferred against the specific organism -- one of a great number -- that caused the initiial outbreak. If a daughter colony was maintained free from infection, and specifically the original infection, genetic drift would act as described above.
Writing this gave me a pleasant break from scrubbing the top of my refrigerator, which refuses to give up its grime without a struggle. Thank you.