Follow the below steps within the Game Server Control Panel
1. Run backup (click here to see how)
2. Don’t power server back on
3. From File Manager download Valheim_Plus configuration files in /BepInEx/config & any other individual files you will need
4. You do not need to individually backup the world files but you can if desired
5. Go to Configuration > Advanced & Press Update Server, this will update BepInEx/Valheim Plus with the latest version, including the valheim_plus.cfg
6. Once complete navigate back to /BepInEx/config and update the Valheim_Plus.cfg with the settings you wish.
7. Start Server
The reason we do not recommend restoring your old configuration file back in to /BepInEx/config after an update is because currently when you update Valheim Plus, it will overwrite your configuration file in /BepInEx/config with a template default. This is because as updates are released more options will be added to the configuration file. This way you will have visibility of the newer options that you wouldn't see if you restore your older configuration over the top.
One easy way to merge your old configuration with the new one is to use this tool https://valheim-plus-config.web.app/
If you missed any individual files from step 3, you can download the full backup from Management > Data Vault and extract that on your PC to gain access to the individual files from the backup