Oh, for God's sake. Unflagging was added because sometimes people hit "flag" by mistake, and I know that because I was one of the ones who asked for it. (Well, the "flagged" list on your profile page was so added. Unflagging I assume has existed about since flagging, but if you accidentally flagged from the homepage, that could not be undone until lately as I describe, because it would also hide the flagged story. Excuse me, I am as yet pre-coffee.)
I'm similarly familiar enough with the lead HN dev, with whom I have passed a friendly discussion or two of how some site features are implemented, to be quite sure unflagging reverses whatever specific moderation weighting flagging applies.
Do you have any specific knowledge to substantiate the claim you have made here?