Unfortunately there is not a setting in Backup Assistant to override the phone, but the system should recognize that you made changes online and remove the contacts from the phone. I would recommend deleting the duplicates from the trash. Also, Gmail may be contributing to the duplicates if you have Gmail contact sync checked. Try unchecking contacts in Settings>Accounts>Gmail, unchecking contacts. You check contacts again after syncing with Backup Assistant, or just use one backup method at a time.