How does comment voting and flagging work?
It seems to me SO just hides the flag feature on that comment for the user after he flags the comment.
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The moderator tools and the 10k tools (available for those with more than 10k reputation) show the flags (but neither one shows who flagged). A moderator can delete it right away, and 10k users (and any other user who happens to read the comment) can then flag the same comment too. When some threshold is reached, the comment is deleted. This does not affect reputation.