It just happens when the server starts. That is the only step, and turning it on has the same result. That is reproducing. It is making the bug appear again. So I am reproducing it.
Just turn the server on, and the area is just... There.
The bug WAS reproduced in Vanilla.
I can't contact the server owner to get it vanilla at this moment, however, we tested it in vanilla earlier today. Here is a crash report with the mod installed, if it helps.
Not at this moment, but we tried uninstalling the mods. The problem persisted in vanilla Minecraft.
This has happened with no mods as well. In a clean Minecraft.
I was getting the server.log, and I find the error. It's not a bug in Minecraft, or anything, simply an OutOfMemory error on my part. I'll allocate more RAM 😛
I'll do that when I get back to my PC, but the problem disappeared again. The first time I witnessed it, it also disappeared, but it reappeared shortly after.
I found out what happened. The server crashed during a save and corrupted the world.