A little update on this issue. I was also running a 1.13.2 Spigot server too, when this bug occured. Whilst we were on the Vanilla jar the Nether was reset, BUT when I switched over to a Spigot 1.14 (BETA) the Nether RETURNED to what it was before. I did not change the world or anything. It just appeared again.
A little update on this issue. I was also running a 1.13.2 Spigot server too, when this bug occured. Whilst we were on the Vanilla jar the Nether was reset, BUT when I switched over to a Spigot 1.14 (BETA) the Nether RETURNED to what it was before. I did not change the world or anything. It just appeared again.