Unless you manually place a file somewhere on the Zune, when files are transferred to the Zune, they are stored in folders appropriate to their filetype (e.g., MP3 files are placed in the music folder). The Zune will allow the same file to coexist on the hard drive, just as long as the file properties (e.g., artist and song title) do not match. The best way to ensure that you delete the duplicate files (and only the duplicate files) is to manually search for and delete them yourself.
Instructions
1. Connect the Zune to your computer using the included sync cable.
2. Wait for the Zune to be detected by your computer.
3. Click "My Computer." Click the Zune icon. Click the "Media." folder.
4. Simultaneously press the CTRL and F keys. This will open the search window.
5. Enter the name of the file you want to search for duplicates. If there is more than one file on the Zune with a similar or exact name, they will be displayed in a list on the center window. Right-click the file and select "Delete." Repeat this step as many times as you feel necessary.
Tags: duplicate files, your computer