I should clarify the original question, because a few of the posts I'm seeing were not in line with the intent of my question. I was NOT suggesting those aero lines get reaved. Simply that the phenotype might be abandoned in future generations. There is a huge difference there. Reaving good warrior lines because of problems with a phenotype would be wasteful (and the Clans hate waste).
No genetic lines were reaved to create the Tanker phenotype, or the aero phenotype, or the Elementals. Existing DNA was manipulated. You use that raw material to create. There is no good reason to destroy it. Altering/abandoning a Phenotype doesn't demand you throw out DNA, you just keep manipulating it.
Hypothetical example....Pilot Alice Rhyde (Current generation) is an aero phenotype pilot. The scientists and Clan Council decide to abandon the Phenotype. Maybe when a sibko is made of Alice Rhyde those sibkids DNA steer more toward the direction of the mechwarrior lines, possibly through the selection of a mechwarrior gene-father, or just straight up changing the breeding protocols. If all the aero bloodlines did this, within say 3-10 generations all your pilots start to look a lot more like mechwarriors or normal humans. Or something radically different because you start to experiment again in another attempt to create a distinctive phenotype that will be more successful this time. Maybe the end result isn't so radical as the scientists try to find a comfortable middle ground that retains some of the benefits but offsets some of the weaknesses.
The phenotype is a result of genetic experimentation, its the result of a set of breeding protocols. The scientists tinkered and engineered to get to this point, so you "un" tinker, or tinker in a different direction. The phenotype either changes into something utterly new or stops becoming so radically different and starts to draw a line toward more familiar territory (like the Ghost Bear lines).
That's what I meant by the question.
If abandoning a phenotype meant reaving all those lines it would never happen. It would never get the votes in any Clan Council. In the Clan Council you don't sell this as a failure "and now lets throw out the resulting trash". No you say, "We tried that, it has not worked as well for our pilots as we had hoped. So even as we use these breeding protocols for our Protomechs, let us steer future generations of aerospace pilots toward a path that may be more successful."