Comment by dang

Just to clarify one misunderstanding: most flags on submissions (nearly all actually) come from users, not mods. So if you see [flagged], it's almost always there because of users and in many cases the mods haven't even seen it yet.

But there are other ways besides flags for stories to fall suddenly off the front page: software penalties (e.g. the flamewar detector, a,k.a. the overheated discussion detector, various abuse detection systems, etc.) and moderation downweights. Users don't do either of those.

These points are covered in the FAQ although necessarily tersely. See "How are stories ranked?" and "What does [flagged] mean?" - https://news.ycombinator.com/newsfaq.html