I’ve just had this issue twice on my 2nd flight with the V2.0 4.8kWh battery. Here’s a video of the incident.
My first flight was 44min without incident other than the old “Battery Error” issue I had with the V1 battery.
In an attempt to resolve the battery error issue, I updated my remote from 5.6 to 5.7 and used the APD tool to disable logging.
On my 2nd flight, after taking off I had set cruise at about 10kW but 1-2 min later, as I tried checking the BMS app, the motor shut down and the ESC started doing the 6 beeps thing. Luckily, I was able to regain power by turning the battery off and on.
Unfortunately, the engine shut off again just 20min later while I was cruising at just 3.1kW. I was able to restart it the same way as before and fly another (slightly stressful) 35min without incident.
The BMS app looked completely normal and I had never experienced it on the V1 battery so I assume it was something to do with the software changes I made.
I’m going to try reverting the controller back to v5.6 to see if that changes anything 
UPDATE: It seems like @nfairfield has figured it out in this post! It’s caused by RF interference.
Both of my incidents happened as I was holding a phone next to the controller. It seems obvious in this second clip because it cuts off just as I pulled out my phone and held it against the controller.