Usually you set up Bouquets, favourite folders, for easy access, to your channels, so you shouldn't notice any duplicates.
If you want to delete them the easiest method is using Dreamboxedit:
http://www.vuplus-community.net/board/forums/vu-tools-settings.10/
Set up a new folder, on your PC's desktop, called settings, default location, and name.
Start up dreamboxedit.
Enter your receivers IP Address, in options, under Tools, go to file and fast FTP download, which downloads your channel list, from your receiver, to your PC.
Edit the list, then save it and FTP it back to your receiver.