That's just the way things go. "Old" names will always hang around, and it's unlikely that will ever change. So knowing (and using) both is the best option.
I donated seed under "Coryphantha vivipara" because that is the species' accepted name in the FOA (Flora of North America). I see though, that it is offered as Escobaria vivipara in the NARGS Seed ex. Laura uses different references, I guess, and that's okay. I know cacti aficionados like to keep the "Escobaria" designation because it makes it easier to differentiate the types in the shorthand of Botanical Latin. I do the same thing with Lilium for my records, too. There will always be new classifications spurred by new technology and study, and even if a new designation system is devised that could deal with the continual changes, you'll still need to "know it all".