I'm pretty sure I've mapped it correctly. It seems like every time it updates, it overwrites all of the server files, including the savegames directory and the enshrouded_server.json. I tried creating a separate directory for the savegame, and that does actually persist between restarts/updates.
When I came home today, I noticed that it had reset once again. What surprised me was that this happened while running.
I've minimized the amount of damage done for when this happens, but I need to reconfigure the json every time.
Any ideas?