I had to reset the NVRAM on my 2013 MB Pro Retina running Sierra 10.12.2 because of problems with Mail.
I had previously gone into Terminal and modified System Integrity Protection as instructed to run TS under Sierra.
On restarting I get the TS grid icon in my task bar but with no space number showing. A four-finger swipe up reveals all my nine spaces and a three-finger swipe changes space BUT I've lost half my hot key configuration so can only switch between spaces left or right (not up or down) with the three-finger swipe.
Going to TS Preferences I see that my hot key combination (Ctrl/Arrow) is still set.
How do I get full functionality back?