Based on what they advised you here:
I take that to mean that they’ve had a tree growing in their orchard for years that they were originally told, and absolutely believed, to be named “Apple A”. They perhaps grafted and sold trees named that, cut and provided scions of, etc.. Only to later learn that that’s not what it is, it’s actually “Apple B” per DNA sequencing and sequence comparisons.
So to my understanding Horne Creek is not saying that “Apple A” and “Apple B” are the same thing.. Nor that “Apple A” is invalid and never actually existed.. or anything of the sort. Simply that they had a mislabel and what they once thought they had, turned out to be something else. Good chance multiple other people are growing actual “Apple A” trees, sourced from someone other than Horne Creek.