Multiple entries after moving files

[TheDreadPirate]

You are not missing anything. I've encountered this issue myself and the only way was to remove them manually. For TV shows, the easiest way to deal with the dupes was to remove the media out of the library at the new location then scan the library. This way only the phantom episodes were present. Then I "delete media" on the show that had dupes and this purges the phantom entries.

I then moved the show back into the new location and the dupes were no longer present.

AFAIK, there is no way to automatically deal with this issue.