I figured it out myself... and since it was non-intuitive and despite my searching not on this forum... here's how I did it. Just a recap... I had duplicate contacts and Calendar events after an upgrade from BIS to BES Express. I could not delete the contacts or calendar using the Desktop Manager> Backup and Restore >Advanced > Clear as they were grayed out in the list.
Go into the service books on the BB
1. Delete the service books for Desktop[SYNC] and Desktop[CICAL]
2. Now go to Blackberry Web Desktop Manager> Backup and Restore >Advanced > and Clear Address Book-All and Calendar-ALL (they are no longer grayed out)
3. Now go to the Blackberry Web Desktop Manager > Advanced Settings> Troubleshooting > Resend Service Books
4. After about 5-10 minutes the Blackberry will start the wireless synchronization over again. It can take up to an hour to synchronize if you have lots of contacts (I had 900) so be patient.