Seeing 2 folders for drives after upgrade

During the upgrade your server has gotten a new “identity” (no, the “friendly name” is not the ID).
This happens if the preferences.xml in the Plex data folder is deleted and recreated afterwards.

So now you have 2 identically named servers on your account.
Find the older of the two here https://app.plex.tv/desktop/#!/settings/devices/pms and delete it.

You should backup the Plex data folder and restore it onto the new machine next time.