Today, I downloaded LuckPerms and added it to all my servers and BungeeCord. I made a MySQL database and set everything up and it's working very well, except that LuckPerms doesn't work with WorldEdit for some reason.
I tried updating WorldEdit, restarting the server that WorldEdit is on, but nothing I tried worked. When I use the command /lp tree, there are no WorldEdit entries. It works perfectly with other plugins though. I checked if there were any previously reported issues about this, but all I could find was an issue from someone who tempered with the WEPIF file. To make sure that I'm not experiencing the same problem, I even tried deleting the file and restarting the server so that it would generate a clean new WEPIF file.

What version LP / WE / Sponge are you using?
Check /lp verbose when you using WE commands like //set

sorry for stating the obvious, but did you add the WorldEdit Permissions? If they don't show in the tree or the editor, then it sounds like it would be a quick fix to just re-add them or import them from a backup or another server.

I'm using BungeeCord 1.13 and all the other servers are running "git-Spigot-642f6d2-6103339" with Spigot API 1.12.2-RO.1. LuckPerms is version 4.2.58 on all servers. WorldEdit is only on the main Spigot server, version 6.1.9.
I tried /lp verbose but nothing shows up when I try //pos1 or //set.
It seems like there's no communication between WE and LP at all.
I'm also using WESV for visualizing WorldEdit and AsyncWorldEdit.
EDIT: I do not use Sponge and I'm running Minecraft version 1.12.2

Do you have any other permissions plugins installed on your server?

It seems that WorldEdit doesn't run any permission checks when you're opped.

You need to set no-op-permissions: true in the WorldEdit config file for it to check permissions as usual.