GM joining as player with a Server Restart

So I set a player to assistant GM through the foundry user management. He then joins as a player and so do I (normally GM), Setup Player Configurations and permissions, dice etc. When I have to restart the server for updates or to play a different system we lose all the settings, actor permissions, and dice and have to rejoin as player again and redo it all. This is a bit of a pain with a large population of PF Society PCs.

Is there a way to avoid this or a setting I am missing?