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When I upgraded to macOS Sierra, a lot of my menu bar icons were duplicated. This included time, wifi, AirPlay, and Notification Center. I've been able to remove all of them except for Notification Center.
Drat... shortly after I posted this I found a way to kill off the SystemUIServer which was just the kick it needed.
killall -KILL SystemUIServer
PS: I searched before I posted originally. :)