What happens if one or more rotors are stopped during autorotation on a quadrotor?
After watching the video the problem he was having was in keeping it horizontal. It appears that the software isn't able to control the unpowered motors.

I know absolutely nothing about quads but I'm assuming with a fixed rotor pitch they must use variable voltage to the motor to control everything such as translational movement. I'm also assuming they have an accelerometer to determine pitch. The first question is how accurate the accelerometer is at low g's. 

Second, when in free fall if a rheostat that is controlled by the computer could be connected across the sides of the motor then your problem could be solved. The freewheeling motors will create a voltage just like a generator so a rheostat would be able to control the current and thus the mechanical resistance to the motor. The rheostat will have an inverse relationship with the mechanical resistance (more electrical resistance less mechanical resistance). How linear that relationship is you'll have to experiment with. If you have the software switch to controlling that resistance it should be able to direct the freefall in the same way it does everything under power, only it will be more limited In its authority. If you do it right you might even be able to use the power generated to recover a little bit of the energy from the fall to charge the batteries like a hybrid car does. 

Like I said, I know absolutely zero about quadecopters so I can't fill in any details, but it seems feasible.