The quickshifter sensor module has failed on my 1299s at 1100mls. Mid ride just stopped, tried resetting electronics but seems it was a good old fashioned component failure. It's getting replaced under warranty so no big issue. The interesting thing is how quickly you had got used to it and how bad it felt without it (1st world bike problems).
I don't use mine very much, tbh at 1000 miles myself I'm giving the gearbox chance to bed in. But out of interest does it show the DQS logo on the dash still or did it think it had been unplugged?
Crap, a rare-ish failure then! I know they are sensitive to getting jammed up with chain lube and sticking so make sure it's cleaned up well