UPDATE 2017-04-25: this solution came in handy when I had another glitch with Sierra: keys would lag or repeat very erratically. Tried resetting pram etc to no avail, so then I performed these steps out of desperation and it all went back to normal.
After upgrading to El Capitan, my Kinesis Freestyle 2 Bluetooth keyboard had a small issue, which I'm documenting here in case other people hit it.
Basically, after installing the OS update, F*/special keys were dead. Solution:
- Open System Preferences -> Bluetooth
- Click on the X icon to the right of the keyboard, in order to un-pair it.
- turn the Kinesis off, then on again, and press the CONNECT button at the back of the keyboard
- The keyboard should pop on the screen, select it and pair it again (you will have to type a few numbers shown on screen)