You need to set it to the same height it was set to originally, since all the cutting is in reference to that Z-axis value. If you set it to the height of the material and there's still some left, set it to that. If you've cut away all that material, then you've got to reconstruct where it was, by going to a part of the program with a known X/Y location and height, touching off to that point, and setting the Z axis to the value shown in the program.