So, the Gcode numbers displayed on the Mach3 screen do not change. But when it cuts it will cut to the smaller size.
Hmmmm I need to find a DXF test file that is smaller than my cut area then do the scale, regen then cut and see if it really changes. That way if it didn't change the size there won't be a problem.
It seems funny that after scaling you just have to trust it because there isn't any visual indication that it did not really resize the object.