I did a fresh install of OMV 3 and while this picked up all the drives, raid, etc.
lex was not working as expected sadly.
I did select an internal drive on the Plex plug-in (the same drive containing the Plex DB) on my OMV 2 installation, however it was starting as a fresh Plex Server and did have any data.
It prompted to add libraries and did not show any movie/music/tv show.
I have checked and it seems it was starting from /var/lib/plexmediaserver as opposed to /media/UUID/plexmediaserver.
I was tempted to create a symlink in /var/lib so that plexmediaserver pointed to /media/UUID/plexmediaserver however I was unsure if this was going to break any functionality or mess up the upgrade.
I ended up re-imaging the OS drive using a back-up from last month, made with Clonezilla.