Those articles were all flagged off the front page, not many people got the chance to see them in the first place. Whoever claimed this was a dupe was just being dishonest and possibly malicious.
I understand your point that if a submission hasn't been widely seen subsequent submissions shouldn't be marked as a dupe. That said, HN is curated, both by the mods and members. It's not purely a popularity contest or a democracy. Members may (and do) disagree on the curation methods, but the curation methods don't require a certain threshold of visibility for any given piece before taking effect.
Marking a submission as a dupe serves a different purpose: it provides a pointer to the "canonical" submission for a given discussion, and not just for those that have spent some threshold of time on the front page.
You may very well disagree with the effects of HN curation in general or for this submission in particular; however, I think it's valuable to recognize that marking submissions as dupes and flagging/downweighting are independent.
Marking of a submission as a dupe that was previously itself flagged off the front page is patently dishonest. Of course, HN is curated, its members can curate however they want, for whatever reasons they want, and those reasons are not always going to be good ones, which in this case they obviously aren't.
Marking a submission as a dupe serves a different purpose: it provides a pointer to the "canonical" submission for a given discussion, and not just for those that have spent some threshold of time on the front page.
You may very well disagree with the effects of HN curation in general or for this submission in particular; however, I think it's valuable to recognize that marking submissions as dupes and flagging/downweighting are independent.