Are you sure that you are deleting a duplicate file? Perhaps you are just deleting a Shortcut to that file. Try Right Clicking on the "file" and see if the properties are the same for each of the "duplicates". There may be a file size difference and/or one might show as a Shortcut in the file properties.
1. Line 1
2. Line 2
3. Line 3
Just testing numbered line entries. That was a bit of a pain!