I think your prediction is wrong. I think that if that happened, the scientific-and-skeptical community would go through something like the following steps:

First, everyone would strongly suspect fraud of some kind. So there'd be a lot of attempts to check this -- from scientists and from Randi-type debunkers. Ex hypothesi these would not in fact detect fraud.

At this point we would have a very well verified phenomenon that's fabulously difficult to fit into the standard naturalist/reductionist framework -- the only way we know of for whether someone has been validly ordained as a priest to influence what happens is via some kind of mind that's able to work with concepts like "priest", "ordained", and "valid". So somewhere around here I would expect the great majority of scientific skeptical types to conclude that something is paying attention to human religious rituals. Might be God, might be aliens with eccentric interests, might be some sort of superpowered AI whose existence we never noticed, etc., etc., etc., but it seems like it has to be something with a mind and with abilities that go way beyond ours.

It would be worth checking a few more-reductionist things. For instance: just what changes to the process of priest-making suffice to make transubstantiation not work? (In many traditions, and in particular in those traditions that believe in transubstantiation in our world, priests have to be ordained by bishops, and bishops have to be ordained by other bishops, and the process involves a ceremonial laying on of hands. Is it possible that there's some thing that gets transferred when that happens? That would be interesting, and might make some of the more-natural options look a bit more plausible. On the other hand, does success depend essentially on intent everywhere down the line? That seems to require non-human minds watching.)

If someone comes up with an actually-working theory about chemical reactions, that would be very interesting indeed -- but it would need to be a theory that explains why the process only works for priests, and only when they are performing a eucharistic ceremony. Otherwise, it's going to be much less plausible even to the most thoroughgoing skeptic than "a god did it" or "superpowered aliens did it".

Distinguishing between the various kinds of superpowered nonhuman intelligence that might have done this thing would be tricky. It seems like it would need to be either something rather like the god of Christianity, or else something deliberately masquerading as the god of Christianity. That might already be enough to justify adopting Christianity as at least a working hypothesis.