When comments get deleted, there is never any notice or any indication of deleted comment. Nobody but moderators can see deleted comments.
If you successfully posted a comment, and did not delete it yourself, that means it was deleted either by a moderator, or by an automatic process. Flagging leads to deletion if one of the following happens:
- Moderator handles the flag and decides to delete the comment
- The comment gets $3+(x/3)$ flags, where $x$ is the score of the comment. Then it's deleted automatically.
- The comment matches a pattern that makes it eligible for autodeletion with a single flag. See What is the SE version of Seven Dirty Words? for the list of known patterns (NSFW).
It's also possible that moderator's attention was drawn to the post by something else (e.g., a flag on another comment), and your comment was deleted in the process of clean-up.
General reference: How do comments work?