Does it just delete the comment? It seems that way, because I recently flagged a couple comments on one of my projects, and then the comment count went down immediately. I also logged out and the comments weren't there.
Do we have a moderation team that can read reports within a few seconds or does it just delete the comment?
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In your case, the comment get's deleted, but a report to the Scratch Team is also generated at the same time.
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