Does the refund require you to return the kitten, or a gesture towards his ongoing veterinary care?
My very first SV was diagnosed with a serious heart defect, his breeder didn't want him back but gave me his purchase price towards a breeding female...so in effect replaced him without me returning him. That's not the contract but more the ethical thing that she did. There was no way I'd be returning him though... I believe he was meant for us because we were the type of folk to undertake the kind of care he needed.
With a replacement though, I would be concerned about HCM if there is an indication that this is not the first kitten from that cattery....so I would think it a risk. Maybe if she can offer an unrelated kitten...not sure how many breeding cats that breeder has to know if that is an option. I'm glad to know that you did get a reply though!
I would not agree that studs that produce HCM should be continue to be used. In fact, generally when there is a genetic health defect in a litter the advice is to neuter the stud and continue with the queens. This is because in terms of DNA, a stud will produce more kittens hence is of greater concern. Agreed that being a young cat developing HCM it is most likely more than one gene is involved :-(
As to murmurs, it is true that some can fade...but if I remember rightly your kitten had a Grade 5-6 murmur which is pretty darn strong! Mostly I think it is the 1-3 grade murmurs that tend to fade with growth.
It is true that many breeders do the vaccinations etc themselves, and in this case she might not want to admit initially that she had not had him vet checked before leaving. It's not how I do things, but then I am paranoid because of my first Savannah!
In terms of saying she is registered with TICA, her cattery might well be registered and she may be registering kittens. TICA is only a genetic registry and hence would not get involved in such a situation. If her cats are TICA registered though she can most definitely obtain 5 generation pedigrees on them.