mtwieg, duty cycle is (on time)/period, so d=0% means every FET should be turned off. The first case is what I want, when I say that I suddenly turn the potentiometer so that d=0%. Problem is in the transition of duty cycle from non-zero(let's call this d_initial) to zero (see example in my previous post), because sampling of the pot voltage happens so fast (16kHz) relative to how fast I turn the potentiometer, the controller will surely feed the low side MOSFETs with some PWM with duty cycle 0<d<d_initial that WILL cause the motor to boost.
Here's some concrete numbers to illustrate what I mean, still using the previous example I mentioned. Suppose before applying the sharp turn in the pot, Vbat=48V, Vemf=36V and d=75%. THEN I apply the sharp turn that commands the controller to set d=0%. Because of the 16kHz sampling, the change in duty cycle will not be instant, and so along the transition, the duty cycle will have intermediate values such as 70%, 60%, 50%, 40%, ... 0%. The back emf does not change instantaneously, and so what happens is somewhere in those intermediate duty cycle values, the motor enters regen mode.
chuckey, I understand what you mean. But I do not want the motor to regen at all times.