Seems like that may have happened with this very substantive Bloomberg article today as well, worth reading, "How Women Got Crowded Out of the Computing Revolution": https://news.ycombinator.com/item?id=15058338
It was on the front page then disappeared quickly, then flagged and unflagged. I fear however that by the time it was unflagged it lost momentum and never had a chance to make it back.
Here's a thought: Would it make sense to reset the decay rate for unflagged articles to counteract such effects?
Usually the answer given to the question "why is this article on the front page" is "because users upvoted it".
Now it seems what users think does not matter.
What difference does it make if it is the same system or the separate one? I am talking about users' will being ignored there on the whim of someone, just because s/he knows better.
Flagging is - as far as I know - not intended as some system to impose the users 'will'. HN does not allow downvoting of submissions. Flagging is a mechanism to remove topics which are off-topic and/or low-quality from HN, not to remove topics some people don't like.
Flagging allows a relatively small number of users to bury a story before most have had a chance to see it. Often this is good, sometimes it isn't. In HN, it's the mods right and duty to override when latter happens.
I get how fun it is to do the long jump, but given that we're talking about something that happens less than 0.0001% of the time, it seems fair to expect a bit better reply quality than this.