To summarise, there are two distinct points here. One is resolved IMO and the other is somewhat unclear.
1. Are the current F1 gearboxes "seamless" ie no interruption to torque transmission? This is resolved - there is no interruption during upshift. There is a period when BOTH gears are engaged and load is shared and progressively transferring from the lower gear to the higher gear. When the load on the higher gear reaches zero, it is disengaged before the backlash has taken up and negative torque begins. Whether this is done with precise actuator timing or a mechanism that disengages the higher gear on overrun is not 100% clear.
2. What happens to the energy released when the engine is rapidly slowed by 15% or so (even if switched off) during upshift? There are a few options - a brief clutch slip, a brief harvest with the MGUK, a spike in torque output (how much energy are we talking about ie what is the rotating inertia of an F1 engine?