https://gist.github.com/Febilian/b9be22b848494c7a06dc130a4fdfbd4f

If you've got any ideas as to what might be causing this, please let me know.

Hmm, the only thing I could think of is that when the chunk unloads, it tries to get the unloaded chunk, causing it to load again, in an infinite loop. Not really sure though

Quite possibly related to this, the server hang + an inevitable crash because of ticks taking more than 60 seconds is consistently reproducible on my private server and in single player by having a player enter the Nether during a session of uptime and then return to the Overworld. Removing Crystals stopped the issue entirely.

Usage of the /forge tps command indicates that the Nether never unloads and its tps drops far below 20 after the player leaves, dragging down performance of the rest of the server.

Even more interesting is that if the player goes back into the Nether before the hang/watchdog crash, tps returns to normal for both the Nether and the Overworld(20 for both). Aka: the issue seems to be happening when a player leaves the Nether(through a vanilla portal, mind you) after having loaded it, like it's having a huge amount of trouble unloading properly.

Yeahhh.. that is bad. I'll take a look in a bit hopefully