I can’t really say with 100% certain since a custom plugin was used and things my be different for you, however, if you post your “rc.conf” (only the line relevant to plex) and ls -l /usr/share/ | grep plex I might be able to at least of better advice!
In any case provided you don’t delete the “plexdata” dir (usually kept in /usr/local/plexdata (or plexdata-plexpass) it should always be possible to install the pkg/port and point it to that (you could also create a new jail, install with pkgng and then copy over that dir; then start plexmediaserver.
I’m curious why the change in the rc.d file didn’t work though most users seem to be running happy with that change and keep on using the PMS_Updater script!