Because it's just not cricket?...It could be done but OP needs to consider what they want to achieve and in what timescales
1. do they want the NC to "go away"?
Either do what the auditor wants (quicker, may lead to problems down the road)
Complain to the NB (slightly longer)
2. do they want to state compliance with the harmonised standard or the newer standard on DoC
if newer standard...just state it and complain to NB in option 1
if the harmonised standard (I do not know the standard so excuse my comment if wrong), it is preferable that the report references it, but with the gap analysis, if it demonstrates that the new standard is tighter and the product is still compliant with the harmonised standard, then I don't know of any reason why you can't claim compliance with the harmonised standard.
e.g. (horendously simplified)
new standard requires result = 5+/-0.1units
harmonised standard requires result = 5 +/-1unit
compliance with new standard automatically infers compliance with harmonised standard
One thing that they MUST do, is demonstrate compliance with the ER's, this would be achieved by conducting a gap analysis between new version and the harmonised standard and justifying how the differences still comply/do not impact compliance with the ERs
Personally (without having any awareness of the business priorities) I would conduct the gap analysis to demonstrate compliance with ERs, reference the new standard on the DoC (because I don't fully agree with referencing a different standard from the one in the report) and tell the auditor to learn the rules, with a request for review of the NC to the NB.