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As per the question title. Comment Flags are not longer affecting flag weight, so this request is now useless.

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I flag comments all the time. Especially those obnoxious ones where people complain that the user doesn't meet their arbitrary accept rate threshold, and therefore they're not going to try to answer their question. – Cody Gray May 6 '11 at 11:20
If they don't hard delete comments from db, this should be possible. – YOU May 6 '11 at 11:44
Comments are soft-deleted, but I believe are only visible to developers. – Jon Seigel Jun 21 '11 at 16:35
Moderators can see deleted comments for any post on a special page. – user149432 Sep 2 '11 at 8:45
up vote 1 down vote accepted

This now happens as shown in More informative flagging history for comments.

Previously, it seemed that comments were deleted but there was some work done recently on how flags are stored. This can now be found in your flagging history.

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