2 Plex Media server folders / 2 Metadata folders, which do I backup?

The red encircled folder is non-default.
Inspect your Windows registry. Look out for the key and its content which is mentioned here: [HowTo] An extended guide on how to move the Plex data folder on Windows

If the key does not exist at all, then the default location of the plex data folder is used. You can probably remove the folder with the #.

Did you experiment with backup and restore of the plex data folder in the past?
Did you use 3rd-party apps or scripts to do that?