Best guess? We don't know.
The link you provided has some good info:
"Revelations" was written by Kim Newton, who would go on to write one further episode of The X-Files: the third season's "Quagmire". The episode was directed by David Nutter and would be his final episode of The X-Files
So, two members of the production team no longer had anything to do with the show. This means it's unlikely anyone else felt it necessary to tie this into anything else, and this episode stands as more of a monster-of-the-week (or messiah-of-the-week) than anything.
The X-Files Wikia doesn't even bother to have a page about the boy, only one for the episode, despite having one for Owen Jarvis who also only appears in this episode.
Even IMDb has no entry for the character, so it's unlikely he appeared in any other episodes.
It's not unusual for this show to not follow up on cliffhangers. For instance, in The Jersey Devil the "Jersey Devil" woman is killed by police, but
Unbeknownst to the law, however, the woman had an equally feral child who survived in the New Jersey woods.
That child isn't ever mentioned or followed-up on, either.