Folders not visible when adding media from a HDD mounted at media on Linux

depending on how you mounted those drives, your attempt to grant the plex user permissions might be in vain.
you could edit /etc/fstab to mount the drives accessible to all users or to the plex user in particular. default mounted drives are mounted for the active user (root when mounting during boot up, your own user, when mounting afterwards).
also… avoid mounting your media inside the /media directory :wink:

There’s a whole section of Linux tips and tricks in the tips, tricks and how-tos forum.