It is unhelpful in the extreme to suggest that EC 261/2004 applies to non community (EU) carriers on flights to the EU. A plain reading of the Regulation which can be found at the source, the Wiki or any number of threads on FT and elsewhere, will tell you this.

EC 261/2004 applies to the operating carrier. The operating carrier which downgraded op was NH. NH is not an EU carrier and this was a ticket HND-CPH or the downgraded segment HND-MUC however you want to look at it. Either way, Japan is not in the EU so the Regulation does not apply.