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.
Ask Different is a question and answer site for power users of Apple hardware and software. It only takes a minute to sign up.Sign up to join this community
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. :)