I created a plugin that installes other of my plugins as APIs. The Problem is, LuckPerms does not find the permissions of the plugins. (ik, i can search for the perms manually but luckperms is easier). When I install the other plugins, I use the pluginmanager and load+enable them. Reloading/Restarting does not help, because the APIs get reinstalled to have always the newest version. Any Ideas how I can reload the system that recognizes the permissions with the luckperms API?

NOTE:
I enable the APIs after the server has loaded and before the server is done enabling

This should work fine already, the permissions should be picked up by LuckPerms as they're enabled.

Does your API loader plugin replace the PluginManager with reflection? That could potentially be the cause of the issue?