Yeah, thats what I meant, Plex really just looks at the SxxExx for the season & episode info. Using folders just makes it tidier.
I don’t use a NAS, so I’m kind of guessing. If the permissions look right, then I’m running out of ideas. I have had problems in the past where I’ve added episodes and Plex doesn’t pick them up. Sometimes doing a “touch” filename triggers Plex to scan the files again.
Come to think of it, I’ve read a few posts on here that suggest there is an added layer of trickery when using a NAS. Sometimes Plex doesn’t get notified about files changes/additions by the NAS. Perhaps that is what is happening.
Try doing the touch on the NAS, that should reset the timestamp on those files. If that doesn’t work, try to Plex Dance S4. Move it outside your TV Show folder, wait or initiated a rescan. When that is over, move S4 back to where it should be and do a rescan. Hopefully it will show up then.