Samba, I am not versed in breeding whatsoever, however, I do have personal experience with congenital Mega-E in a GSD which I would like to share.
Before we got into rescue of GSDs, our Max and Koia came from a breeder (excellent West German lines - their mother is a direct import from West Germany and their father is from a well known/reputable breeder of West German VA & V rated show lines). The breeder did not breed Max and Koia’s parents again after confirmation of Max’s congenital primary Mega-E.
Out of the litter of 9, my Max was the only long hair, the only one with EPI (also common in GSDs) and the one with congenital primary Mega-E. The EPI was strictly a life maintenance issue that was treatable and was under control.
The Mega-E was a battle from Day 1. Cornell looked at the radiographs and said Max’s case was one of the worst they had seen. We were fortunate enough to have a wonderful, knowledgeable, vet, as well as the resource of Cornell.
Every day Max had to eat his "mush" vertically. He could not run as long/as hard as his fur siblings, he could not have free water, he could not have certain treats, he had to have his temperature monitored to watch for the first signs of aspiration pneumonia, he had to take medicine every day. Yet, Max was a happy, extremely loving boy every day of his short life.
Even with all the care and precautions above, I had to let my Max go to the Bridge on 2.12.07. He was at Cornell for severe complications from Mega-E - aspiration pneumonia and his stomach had started to come up through his esophagus. We were discussing a feeding tube, however, Max's lungs were not strong enough for Max to recover (4 episodes of aspiration pneumonia had taken a terrible toll on his lungs).
So I said goodbye to my Max one month before his 3rd birthday. Hardest moment of my life without question.
Currently, there is no cure for congenital primary Mega-E*. I asked the doctors at Cornell about a cure and they said it would probably take an esophagus replacement and that is no where near on the horizon.
I would not take back my years with Max for anything. However, with what is known at this point in time, medically and management wise, to knowingly breed a dog with Mega-E (or even to not have her/him spayed/neutered**) is simply irresponsible and uncaring. Breeding is a monumentaly responsbility and science. In my opinion, there is no reason whatsoever to breed a dog with known Mega-E.
*Now, there are several other reasons a dog can have a Mega-E and you can read about those in the links cited above. I was fortunate enough to have a foster come into my life 5 months after Max’s passing that had PRAA, secondary Mega-E. She was able to have surgery at Cornell to correct the PRAA and she is now adopted and living a happy normal life (although she still does eat vertically)!!
**Dogs with Mega-E can/should be neutered/spayed, as long as precautions are taken regarding aspiration.