I don’t think you will lose your configurations by updating, but if you are worried about losing them refer to this article.
If you are worried about losing your watch history as well, refer to this article.
Plex updates never delete your configuration or meta data. You just might have to fix some settings (e.g. library location) after the update. Don’t panic when your server first appears empty or “new” after the update. We will guide you to restore the correct settings.
You might have to migrate from my old dev2day.de package to the “new” official package, if you still use the plexmediaserver-installer package. Please read “Legacy Support and Migration” at the end of the following post: