Well the way our server works, the outer dimensions are actually in separate folders with their own seeds, so they're not tied to the main world. Since we knew that the update was coming, we never did much in the nether , so I just deleted the whole thing and regenerated it. The fact that that would obviously generate a new seed just slipped my mind, but I thought it would still regen the portals as soon as we went through. I've done this before simply by destroying the nether side portal and then having someone else come back through from the other side. This used to be the whole basis for a type of obsidian farm.

Regardless, either something has changed in the code, or it's just a byproduct of how the upgrade process works. I haven't done any experiments yet, but I assume there wouldn't be an issue with a world that was initially created in 1.16, and probably not a problem with one that was simply upgraded as a whole since that shouldn't regenerate the nether side chunks that had already been created.

Honestly, I probably just shouldn't have been lazy, and simply cullled all of the nether cunks except for the ones immediately surrounding our portals rather than just regenerating the whole thing. On the other hand, the videos are way more interesting when weird stuff goes wrong, right?