<p>From my experience flagging still works as expected after passing 3k reputation limit. The little box appears that says certain number of <em>close</em> votes remain, but the question is actually flagged. I infer that, since usually moderators respond and then my flag weight goes up. </p>

<p>The most recent example of that is this <a href="https://math.stackexchange.com/questions/33617/a-sequence-of-order-statistics-from-an-iid-sequence/39391#39391">question</a>. After my bounty expired here I flagged it to move to math.SE. I had more than 3k reputation then. It might be that the behaviour of the site changed since then, but this must be reflected in <a href="http://meta.stackoverflow.com">http://meta.stackoverflow.com</a>. As far as I understand people care about their flag weight, so if there were recent changes there should be a lot of activity related to that.</p>

<p><strong>Edit</strong></p>

<p>I flagged the other question and realised that my answer is not entirely correct. When you flag the question there are several options available, one of the options might get converted to close vote. In this case if you really want to flag choose the option <em>other</em> and write the reasons for closing. This way moderators will certainly get informed, since flagging is done not only for reasons of closing. It will be a little abuse of the system, but for the greater good.</p>
