Instead of the rate of acceleration (deceleration = acceleration with a negative sign) making a step change at the moment that the braking force is applied, it will ramp up as the shaft twists, with the flexible end first overshooting the deceleration and then catching up. If the braking force is sufficient to momentarily stop the flexible end of the shaft, you'll get some really interesting and potentially noisy and violent stick-slip phenomena as the flexible end of the shaft first stops then the shaft twists enough for the torque to overcome the static coefficient of friction which then violently lets go. Presumably this connecting shaft is going to have a non-zero mass, and will thus have a resonant frequency, first overshooting the initial braking position and then stopping again, then twisting-up and breaking free again.