They presumably meant that it’s been downranked relative to what you’d expect from a post with that many upvotes in that short of a time frame. Hundreds of upvotes in a few hours is usually a top 5 post
Afaik flagging acts like a super-downvote as far as the algorithm is concerned
Yes flagging is super downvote
One of my page was 2nd on the main page trending towards 1st, a single flagging pushed it to the middle of the second page.