One of the most common ‘newbie’ problems is understanding how to name and structure your media. (it bit my butt at first too… haha)
the ‘quick trick’ to adding back any entries you deleted (but the media is still there) is simple:
- Open File Station
- Move the item (TV Series or Movie or Music) to a safe location PMS doesn’t monitor (any other share will do)
- Update libraries
- Empty Trash
- Clean Bundles (this removes the entries from the database and the metadata info)
- Move the media back into its original location
- Update Libraries again
We call this the 'Plex Dance" 
