From Denon FAQ:
Why do remote drives and songs also show up in the main collection?
The Main Collection is a complete list of all connected media, both remote and local. This allows for all of your songs on either connected hard drives or internal storage to be used interchangeably, making it easy to find your track regardless of where the file is stored.
Because of this, duplicate entries may appear in the main collection if a song is located in both the main collection and a removable drive. Songs are not physically duplicated on the drive, the main collection is simply reporting the song in multiple databases. Removable drives can still be moved from one computer to another and have their crate structures retained, and any song in the main collection can be dragged to the Engine player for playback and editing at any time.
We realize that this is a departure from more traditional workflows and are working on an option to separate collection drives with remote drives in a more clear manner.