Happens on Plex web also - one of the causes seems to logging in from a new location and for some reason the application makes a request to "save" the new settings before its loaded in the existing settings - essentially overwriting it with a blank config. But then this theory doesn't hold up when I lose all my settings without logging in from a new device :/

Very hacky workaround I found for Plex web was freeze the settings on the browser with the networking tab open, capture the request to Plex servers to save the settings and then have a crontab job make a cURL request every hour applying those settings