You really need to show us how the files are named in these folders and the folder path.
The proper Plex Dance is as follow:
-
Explorer
→ move the file outside the scope of Plex -
Plex
→ scan the library for file updates -
Plex
→ empty trash, clean bundles -
Explorer
→ return the file to its original place -
Plex
→ scan the library for file updates