I don't suppose anyone knows but should I adjust my offsets with the ND filter in place, or will the meter simply be able to compensate? Apologies if that's a dumb question.
No, you don't. The ND filter is only needed to make the exposure time for test stripes more managable. That's all there is to that. I do not have the Zonemaster Calibration manual at hand, but I believe that the use of a ND filter is mentioned as a method of lowering light output when exposure times become too short.
