Is this a position move? If so, once you being a move in order to start a new move you must stop the motion before starting again. Velocity moves can have a new setpoint provided to them before the reach the existing setpoint. When that happens the acceleration will be reduced to 0, and it will start accelerating to the new goal speed. You could look at lab 13e which is velocity moves in position control. This might be a way to realize your application goals.
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