Well, I wouldn't say, disappearing more like... a glitch. I've noticed this recently when I've been building. Sometimes it seems Waystones will deactivate, almost. I've noticed a few of my Global Waystones suddenly not be active. Clicking on them activates them as if I just found them, but using the name I already assigned to it. It has become a big problem, as I can no longer return to a large construction project I was working on.
I've tried relogging but to no avail.

I'm currently running this with RLCraft, and a few other mods.

This was a common issue with Global Waystones in 1.12 and they weren't really supposed to be used for player usage but for server owners. In 1.14+ the whole system got rewritten which should fix most of these weird issues, but due to the large size of the changes, they won't be backported to 1.12.