Had to reset NVRAM -lost TS hot keys

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?

If no space number is showing, I am concerned that TotalSpaces is not working because SIP is turned fully on.

It should warn you about this, but for some reason we have been seeing cases where the detection (that SIP is fully on) does not work.

If you have reset your NVRAM then I guess SIP could have be reset (the settings for SIP are stored in NVRAM).
So you may have to redo the procedure to partially disable it in order to get it working again.

Thanks Stephen - good support as ever.

I deleted TS2, did the Terminal partial disable, reinstalled and all is working again.