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I don't know too much about Notes. I would assume that these messages were on the device prior to it being activated on the BES. I could be way off here as well.
This can be done via desktop manager. Plug the device into USB port, open desktop manager, select backup/restore, select advanced. When the right panel populates with the numbers from the device, scroll down to messages and click 'clear.'
This will delete all messages on the device, however it will prevent you from wiping the device.