Basically, when I try to remove permissions or parent groups, it has no effect.

Logs:

[19:12:16 INFO]: ptrcnull issued server command: /lp user ptrcnull parent info
[19:12:23 INFO]: ptrcnull issued server command: /lp user ptrcnull parent clear
[19:12:23 INFO]: [LP] LOG > (ptrcnull@freebuild) [U] (ptrcnull)
[19:12:23 INFO]: [LP] LOG > parent clear
[19:12:23 INFO]: [LuckPerms] [Messaging] Sending log with id: a4a387f4-e585-4a65-a642-726c4f550c3b
[19:12:23 INFO]: [LuckPerms] [Messaging] Sending user ping for 'ptrcnull' with id: 366b0f88-016e-494a-b4ba-074dc8565cfb
[19:12:24 INFO]: ptrcnull issued server command: /lp user ptrcnull parent info

I'm using LuckPerms with 4 Paper and 1 Waterfall server, all on v5.0.92.
Snippet of config:

server: freebuild
use-server-uuid-cache: false
storage-method: mariadb
data:
  address: "333.444.555.666:3306"
  database: <db name here>
  username: <username here>
  password: <password here>
  pool-settings:
    maximum-pool-size: 10
    minimum-idle: 10
    maximum-lifetime: 600000
    connection-timeout: 5000
    properties:
      useUnicode: true
      characterEncoding: utf8
  table_prefix: 'luckperms_'
  mongodb_collection_prefix: ''
  mongodb_connection_URI: ''
split-storage:
  enabled: false
  methods:
    user: h2
    group: h2
    track: h2
    uuid: h2
    log: h2
sync-minutes: -1
watch-files: true
messaging-service: none
auto-push-updates: true
push-log-entries: true
broadcast-received-log-entries: true

messaging-service: none

This should be an actual messaging service, as unlike v4 v5 sees "none" as just that: None (v4 did then auto use sql when database was mysql/mariadb). I suggest setting it to sql.

In addition check the consoles of all your backend servers and the proxy for if they received the update ping send by the LP instance, where you executed the command from.

Oh, I migrated from v4 and there wasn't anything about this in the docs.
Nonetheless, the issue was still present on v4... I'll try setting an actual messaging service.

EDIT: but wouldn't the local server show updated parent groups?

Waterfall:

>.... [20:58:19 INFO]: ptrcnull executed command: /lpb user ptrcnull permission info
>.... [20:58:29 INFO]: ptrcnull executed command: /lpb user ptrcnull permission unset test.permission
>.... [20:58:29 INFO] [LuckPerms]: [Messaging] Sending log with id: fb03e08d-da81-4308-a60c-75b1cb2e7952
>.... [20:58:29 INFO]: [LP] LOG > (ptrcnull@bungee) [U] (ptrcnull)
>.... [20:58:29 INFO]: [LP] LOG > permission unset test.permission
>.... [20:58:29 INFO] [LuckPerms]: [Messaging] Sending user ping for 'ptrcnull' with id: f6c18f66-401d-48f6-afef-3433bd97b5c9
>.... [20:58:31 INFO]: ptrcnull executed command: /lpb user ptrcnull permission info

Other servers didn't show anything in the logs.

It did load the messaging service config on all servers though.

Waterfall:

[21:00:18 INFO]: __
[21:00:18 INFO]: | |__) LuckPerms v5.0.92
[21:00:18 INFO]: |___ | Running on BungeeCord - Waterfall
[21:00:18 INFO]:
[21:00:18 INFO] [LuckPerms]: Loading configuration...
[21:00:19 INFO] [LuckPerms]: Loading storage provider... [MARIADB]
[21:00:19 INFO] [me.lucko.luckperms.lib.hikari.HikariDataSource]: luckperms-hikari - Starting...
[21:00:19 INFO] [me.lucko.luckperms.lib.hikari.HikariDataSource]: luckperms-hikari - Start completed.
[21:00:20 INFO] [LuckPerms]: Loading messaging service... [SQL]
[21:00:20 INFO] [LuckPerms]: Loading internal permission managers...
[21:00:20 INFO] [LuckPerms]: Performing initial data load...
[21:00:21 INFO] [LuckPerms]: Successfully enabled. (took 2974ms)
[21:00:21 INFO]: Enabled plugin LuckPerms version 5.0.92 by Luck

Paper

[20:54:23 INFO]: [LuckPerms] Enabling LuckPerms v5.0.92
[20:54:23 INFO]: __
[20:54:23 INFO]: | |__) LuckPerms v5.0.92
[20:54:23 INFO]: |___ | Running on Bukkit - Paper
[20:54:23 INFO]:
[20:54:23 INFO]: [LuckPerms] Loading configuration...
[20:54:24 INFO]: [LuckPerms] Loading storage provider... [MARIADB]
[20:54:24 INFO]: [me.lucko.luckperms.lib.hikari.HikariDataSource] luckperms-hikari - Starting...
[20:54:24 INFO]: [me.lucko.luckperms.lib.hikari.HikariDataSource] luckperms-hikari - Start completed.
[20:54:24 INFO]: [LuckPerms] Loading messaging service... [SQL]
[20:54:24 INFO]: [LuckPerms] Loading internal permission managers...
[20:54:24 INFO]: [LuckPerms] Performing initial data load...
[20:54:25 INFO]: [LuckPerms] Successfully enabled. (took 1502ms) 

v5 sees "none" as just that: None

I think you're wrong:
https://github.com/lucko/LuckPerms/blob/8725ace73939c8c16629f35d17e5c7654a5c855a/common/src/main/java/me/lucko/luckperms/common/messaging/MessagingFactory.java#L56-L58

This issue is particularly interesting. If the issue persisted on v4, the only issue I can think of is with your database user lacking permissions to update or delete records from the database.

Do the grants look right? (MariaDB 10.2.29)
They look right to me, but maybe I'm overlooking something.

the only issue I can think of is with your database user lacking permissions to update or delete records from the database

I was thinking the same, that or maybe your database is in some sort of read only mode?

Does updating permissions work ok? Or is is just removing that one group?

maybe your database is in some sort of read only mode?

I don't think so, other plugins work just fine

Does updating permissions work ok?

Yup, setting permissions works

Or is is just removing that one group?

Removing anything doesn't work, no matter if it's a single permission node or a player's parent group

Have you checked your DB server's error logs to see if there's any errors there? Also, could you try making a new user & the same database and see if it persists, then new user + new database, then new database + same user. That way if all except one of those configs work it'll narrow down the issue, if all of them do not work then maybe either a bug with your MySQL version in particular, or something like that.

Trying to remove a test permission:

# tail -f a3db90093614.log  | grep test.permission
		2617882 Query	INSERT INTO `luckperms_messenger` (`time`, `msg`) VALUES(NOW(), '{\"id\":\"<uuid>\",\"type\":\"log\",\"content\":{\"timestamp\":1584314514,\"source\":{\"uniqueId\":\"<uuid>\",\"name\":\"ptrcnull@bungee\"},\"target\":{\"type\":\"USER\",\"uniqueId\":\"<uuid>\",\"name\":\"ptrcnull\"},\"description\":\"permission unset test.permission\"}}')
		2617886 Query	INSERT INTO `luckperms_actions` (time, actor_uuid, actor_name, type, acted_uuid, acted_name, action) VALUES(1584314514, '<uuid>', 'ptrcnull@bungee', 'U', '<uuid>', 'ptrcnull', 'permission unset test.permission')

It looks like it tries to notify other servers and log the action, but never actually removes the permission.

Also, this is on a new user with current database, same as the old one, it's weird that it works on messenger and actions and not user_permissions though

Just to be 100% sure, the <uuid> is something you've redacted for this issue, right, not a literal <uuid>?

Yup, redacted for clarity.

Does this happen on latest? I see above you're 2 builds behind

It was the latest when I was creating the issue... I'll update, I guess

Still happens.

Have you been able to come up with any exact steps to reproduce the issue? If you install a fresh server and fresh database of the same version, etc?

Okaay. Apparently on a new database the issue no longer occurs.

root@server:~/ptero/db# du -sh minecraft/
2.3G	minecraft/
root@server:~/ptero/db# du -sh luckperms/
768K	luckperms/

Can this... cause the issue?

I'm not sure what I'm looking at there, what are those folders?

These are MariaDB's database files, I think.

Still not sure what you mean by can that cause an issue, what's the issue? The size?

Well, that's the only thing apart from the amount of tables that differs between databases, so that was my guess.

My suggestion would be to create a backup of your data (you can use /lp export for this), then re-create the database from scratch. Sounds like something has been corrupted.