I just upgraded to the newest OS on the 9700 (5.0.0.862) and, as usual, after my first sync, I have duplicates of all my calendar entries. (And, for some reason all of the birthday events in the calndar have disappeared).
There used to be a way to delete these duplicate entries through the Blackberry Desktop Software, but now that I am using version 6.0 for that, I am not sure how to do it.
Delete all email addresses in your BB except the one you want calender toi sync with. Sync the phone. BDM will say XXXXX@XXXXX not found, XXXX@XXXX will be default email address for syncing. Click ok. After sucessful sync go back in to the BB and recreate your email addresses.