What happens from the public's point of view? The comment disappears without a trace.
Yes, the comment disappears without a trace. From other users' point of view, they wouldn't know if there was any specific comment by User A. Only moderators can read a deleted comment. If a specific comment by User A is gone, they will just guess it was either (1) flagged by other users and deleted or (2) deleted by a moderator.
What happens from User A's point of view?
There is no way for User A to know whether his/her past comment has been deleted unless (s)he checks his comment again as there is no notification such as "Your XYZ comment has been deleted". Furthermore, it is impossible to know whether it was flagged by other users or outright deleted by a moderator.
What happens when a not-nice flag on a comment is accepted?
Probably most of the time, the comment will be gone if the flag is accepted. But it wouldn't surprise me if a moderator marks the flag helpful and doesn't delete the comment and only edit out some offensive or irrelevant part.