My question is. What gene defect would prevent a SF from developing a muff & beard? If not a defect, what is the cause? In my state, I'm only aware of two breeders so I was thrilled to get the first set without having to pay shipping. BUT... I'm not convinced that they are quality birds.
Muff/beard is caused by a dominant gene. The same gene causes both of them, but sometimes I just say "beard" or just "muffs" because I'm too lazy to type "muffs and beard" every time.
A chicken with two copies of the muff/beard gene will grow muffs and a beard. Other genes control how large the muffs and beard will be.
A chicken with no muff/beard gene will not grow any muffs or beard. This is probably what happened with your hen Sophie.
A chicken with just one muff/beard gene will grow muffs and beard too. But because the chicken has one muff/beard gene and one gene for no muffs & beard, this chicken can produce chicks that do show muffs & beard (examples: Pierre and one of your current chicks) and chicks that do not show muffs & beard (examples: Sophie and your currently beardless chicks.)
When Sophie produces chicks, she gives each chick a gene for no muff/beard. The same is true for the chicks with no beard.
If you breed the bearded pullet with her no-beard brother, you will get about a 50/50 split of chicks with beards, and chicks with no beards.
If you breed the male with no beard to his beardless mother Sophie and his beardless sister, you will get just beardless chicks. You should not get any chicks with muffs and beards from those pairings.
If the seller has a flock of chickens that show beards and muffs, they will not know if any of those chickens carry the gene for no beards... until they get some chicks with no beards. A chick with no muffs or beard is proof that both the father and the mother have the gene for no muffs & beards, but in a large flock it can be difficult to identify which parent birds are actually involved, and in a small flock they may all have the same problem.
Ideally, all Salmon Faverolles would have two genes for muff/beard, so every chick would have those genes, and you would never see beardless chicks. But in practice, it doesn't always happen that way.
Five toes have the same kind of dominant inheritance: a chicken with five toes could carry the gene for four toes.
Because it takes so many genes to make a chicken with all the right traits, it is easy for an otherwise good chicken to have one or a few details wrong. Sometimes it makes sense to breed from those birds anyway, depending on which traits the breeder considers most important. The breeder may have been focusing on body shape, color, number of toes, or various other details and let the no-beard issue slide a little. Or they may be working a bit on everything at once, maybe by culling all beardless or 4-toed or off-color birds but continuing to breed from birds that carry those traits.
I now have 3 babies who I know both parents were sold to me as SF & I would like to hatch more for selling next Spring. I just want to understand this lack of muff/beard issue.
If the male has no beard, then he will give the no-beard gene to every chick he sires. The bearded female should produce some chicks that show beards but they will still carry the gene for no beard. The females with no beards will produce beardless chicks, and the female with the beard will also produce some chicks with no beard.
If someone wants backyard pets and does not intend to breed, they should be happy with the chicks that do show beards. They may even be happy with the no-beard chicks, especially if you point out the issue so they can decide whether they want those chicks or not.
But if the buyer intends to breed from the chicks they buy, they will probably not be happy with any chicks from your current flock, not even the ones that show beards, because the chicks carry the no-beard gene. (Possible exception: if the birds have really good traits in other areas, some breeders would be willing to work with the no-beard gene while they add those other good traits to their flock. But some other breeders would not be willing to introduce the no-beard gene into their flock no matter how many other good traits the birds have.)
Edit to add: does the male have a beard or not? I just looked back and I don't see where you said one way or the other. If he does have a beard, then he will produce some chicks with beards even when bred with no-beard hens. And a bearded male with a bearded female will produce some chicks with two beard genes (great!), some chicks with one beard gene (they show a beard) and some chicks with no beard (not what you're hoping for.)