Architecture: x86_64

Model name: AMD Opteron(tm) Processor 4334

Ram: 32Gb

Java Version: 8

Linux version 3.14.32

Ubuntu 16.04.5 LTS

Dedicated Server by SoYouStart

I can confirm this issue, I don't use WorldEdit/WorldBorder, it's caused by default world generator.

CraftBukkit version git-Spigot-fe3ab0d-bfb9131 (MC: 1.13) (Implementing API version 1.13-R0.1-SNAPSHOT)

(If you're wondering why this is the case, it's because trees cross chunk borders. So if a tree has its "roots" in one chunk, but you then regenerate another chunk, the tree will be wiped out, but since the chunk with the tree "roots" was not regenerated, it will not grow back into the chunk you regenerated.)

There's no way to fix this when you're regenerating only a single chunk.

As for regen, I don't think that's easily fixable.
Terrain decoration isn't meant to run unless it can also go into the surrounding chunks.

I'll add a note to the documentation about it.
If you or someone else has a fix feel free to propose it.

Hmm thats odd, heres my plugin list:

CoreProtect, WorldEdit, PlaceholderAPI, WorldGuard, ProtocolLib, PowerlessLamps, VoxelSniper, RidableDolphins, FeatherBoard, Zenchantments, mcMMO, CS-CoreLib, Vault, BloodInMinecraft, CrazyEnchantments, HyperDrive, ArmorStandTools, AnimatedNames, Clickssentials, HeadDatabase, Citizens, TradeMe, CT-Core, Slimefun, FurnitureLib, SlimefunLuckyBlocks, SoulJars, DiceFurniture, RPG-Discovery, Essentials, Towny, ExtraHeads, PrivateStorage, CMI, ChestTerminal, CitizensCMD, WG-Operations, WorldGuardExtraFlags, VentureChat, SelectionVisualizer

World looks fine at both those coords.

Sorry, all you have to do to reproduce it is either //regen or go to these coords on this seed:

Seed: -1411370035

Coords: X=1043, Z=550

More Coords: X=1284, Z=757

No reproduction steps (seed + coordinates of affected map).