I thought the fuel and ignition was completely cut while engine braking. Is that not the case?

 

I see in my datalogs that the injector duty cycle is 0% while engine braking.

 

Yes.
However Honda has built hysteresis into the VTEC switch point so that if you switch onto the high cam and then immediately decelerate, the engine will not switch onto the low cam for two seconds regardless of the throttle position.

 

So the "extra" line is really for when you instantly accelerate and it is still on the higher cam, but at low rpm?