I got some workaround and it works perfectly. I maintain a Category for each contact in my contact list. So if I need to delete all the contacts from my BB then I set my filter on Desktop Synch time where I say synch only the contacts with Category='phone Directory" or something that you have.
If I need to delete all the entries then I mess this and change 'Phone Directory' to "Whatevererrrrr Phone Directory" and now I know there are no items with that categ and nothing will be moved from outlook to BB or vise-versa.. so I have nothing in the BB contacts.
Try it .. it works.
By the same token I carry my Nokia phone with me for voice plan so I sync my Nokia Phone using Nokia's sync tool and tell to sync only the phone number whose category is 'Nokia phone directory'. I always add my category for each contact when I add them