A hapless vampire (the undead type because a few vampire stories have them as a separate species from humans), prowling the streets in the dead of night for fresh blood, has a run-in with PER and gets hit with a potion bomb. What do you think would happen to it?

I am thinking Thestral .. if the magic in the potion is enough to guide the nano portion around the differences between human and vamp

Vampires aren't alive, so probably nothing happens. Maybe it absorbs the potion and then starts transforming everyone it bites.

Hmmm… the in-verse analog of a human vampire might be the emotion-sucking changelings, or the magic-sucking Grogar. But the simplest idea would be to have that person convert into a vampony - a blood sucking pony - as opposed to one of Luna’s bat-ponies, which are clearly alive, can reproduce in the normal biological way, and so are not un-dead. As to vampony kryptonite, with the lack of religious symbols represented in the show I wonder what would replace the cross/holy water - maybe a horse shoe and apple cider! The Apple Clan might then be the in-verse Van Helsings!

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I wish I could say it was a "a broken clock is right twice a day" with PER saying they're eliminating evil, but a vampire is a corpse housing a curse. I doubt the potion effects corpses.

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If this happened in my Bureau universe, it would be nasty. Since there is no magic in my stories (technically, not even in Equestria), then the usual, magically powered Vampires of myth and legend could never exist. But - for the sake of argument - if there was a nonhuman species that had evolved to resemble humans, and fed on them (as some spiders have evolved to resemble ants in order to infiltrate nests and eat them), then getting converted would not end well.

In my stories, 'potion', or Ponification Transformation Serum, reads human genes and converts human bodies into Equestrian ones. In a nonhuman species, either of two things can happen. One is, the reaction stops after digesting a portion of the body. The other is that the reaction continues, only the nanomachines are unable to function correctly. The result would look like the most horrible of Transporter Accidents from Star Trek. Bubbling, screaming blobs of nightmare flesh trying to become various random parts of several ponies, at least until the reaction stopped. Then the quivering mess would die, gurgling in pain and agony. Not, perhaps, the nicest way to die.

It would be a heck of a show, though.

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well, potion was created to fix very specific, relatively narrowly-defined human-only problem. Other (more biological than cybernetical, at mind level) beings have separate possibilities.. like barrier itself in late times (from memory "cross the Amazon" had interesting scene of dead human being transformed into quite alive.. bunnies. multiple of them...). But this is late barrier... so being _vampire minority_ is not easy anyway, and even in your universe (but this brings whole amount of new questions how exactly those vampires functionated over time.. how small their population was, what was variation in behavior/thiking, how was their personal evolution over centuries, if any.. humans being humans obviously like to demonize anyone, so i do not think I'll trust 'our' tales on this matter uncritically..)

They would turn into ponies because vampires used to be human. They are just former base-line humans with a weird necro magic thing or super science genetics keeping them sentient and moving.