According to the accepted answer to this faq question: How do comment voting and flagging work?
Comment flagging is 100% automated and does not require any mod intervention.
I believe I saw a flag on a comment (in the 10k tools page) which I thought was offensive (and a mild personal attack, which could lead to a comment war) and I flagged it too. After some time, the flags were cleared (as I could see in the 10k tools page), but the comment remained and the answer (by the same person who made the comment) was downvoted.
The only conclusion I can draw from this is that the flags on the comment were cleared by some moderator, perhaps under the mistaken impression that some idiot flagged the comment instead of downvoting the answer.
Note all this happened within the past 4 hours, so I don't think aging of the flags is the reason.
Why do we have moderators
even looking at and clearing comment flags?
Apologies if there is a more recent thread or if I have somehow missed some feature and drawn the wrong conclusions.
I will not post a link to the relevant comment (so please avoid the 'data or it didn't happen' comments).