flagging impacts the ranking, even before a [flagged] tag is shown, so when you complain that the discussion about this is not on the front page but somewhere deep down the ranking, you are complaining about user flags. (And after a discussion got enough comments, which it did, all further submissions are duplicates in addition)

Of course we don't actually know that, but from what little the HN mods have indicated that appears to be at least part of the algorithm.

But moderators do sometimes manually save a thread from being flagged dead, which apparently they chose not to do in this case.