Lots of possibilities here, but not really enough information to give a definitive answer.
What is keeping track of the pulses from the incremental encoder? What generates the fault? What is the nature of the fault? Could it be a 'rollover' fault where the leadscrew turns beyond the upper limit of the device keeping track of encoder counts?
In general, if you are using an incremental encoder for position control, you need a method of 'homing' the encoder. Typically, that involves moving the axis to a known position and setting the position controller's value equal to that postion. You need to do this if it is possible for the axis to be moved while power is removed from the encoder or if there is any possibility of slippage between the controlled axis and the encoder.
An absolute encoder eliminates the need for performing a homing procedure when power is removed, but would still need to be homed if there is any slippage.
