So, I noticed when editing permissions on my server, they are not applying immediately. I have to disconnect and reconnect my Member (default) account for the permission to take effect.

Example:
Default inherits mem_essentials. mem_essentials has essentials.help set to true. Member has access to help. Owner runs /lp group mem_essentials permission unset essentials.help. Member still has access to essentials /help command. Both players are on the same server. Bungeecord is setup properly. Messaging goes through with no errors. Member loses access to essentials /help when they reconnect.

Also, both clients are running on the same computer... not sure is this will be an issue but worth mentioning.

Same problem here on Spigot 1.12.2. You cannot sync the permissions with /lp sync.
You need to reload/restart the whole server to apply permissions.

Thanks for reporting, should be fixed in the latest version