AFAIK (not done it myself) yes you do need to do both keys.

It says later on in the service manual that you can "void" a key, say if you've lost one and don't want it to get into the wrong hands, by re-registering the one that's left. That would seem to confirm that the standard black keys need to be programmed in pairs - registering just one will cause the other to stop working. It would also appear that having to register in pairs prevents more than two keys ever being registered to the same bike, which also makes sense.

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