That step is important. You do not need to delete permissions, just re-apply with the correct settings.
Not sure why the shows are taking so long to appear. A manual scan of the library should pick them up immediately.
If you like, we can take a look at the Plex log files and see if they show anything.
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Ensure Plex Media Server is configured for debug, not verbose, level server logs (Settings → Server_Name → General + Show Advanced).
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In Settings → Library, enable Scan my library automatically (Plex will scan the libraries when it starts. It also adds some additional info to the log files).
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In Synology Package Center, stop Plex, wait ~20 seconds, start Plex (this makes sure the startup sequence is logged).
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Wait 3 - 4 minutes for Plex to fully start & log the startup sequence.
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Plex Dance Boardwalk Empire.
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If the show still does not appear, pull and post a set of server log files (Settings → Troubleshooting). Upload the full zip file to the thread (drag it into the message window and wait for the upload to complete).
