Comments should be deleted (or flagged for deletion) only when they are no longer relevant.
Once requests for clarification or correction are addressed by the post author, by incorporating or rejecting them, those comments often become obsolete.
However, comments are a multi-axis thing. Upvotes count. If there is a comment with a needed clarification or correction, it may stay indefinitely especially if upvoted.
Example “But the DMG says X which directly contradicts your answer <20 upvotes>”. That stays basically forever, and a flag would be declined (at least by me when I was modding). Or a request for clarification on a super unclear answer that’s getting downvoted - the answer may not be bad enough or get deleted, but then the comment still has value.
The fuzzy line here is that an author may see a critique and reject it but give no visible sign thereof. Ideally the author would drop a comment or flag that comment as obsolete themselves.
So judgement is applied.
- Is the comment jibber-jabber or a justified improvement or request for clarification?
- Is it upvoted?
- Is there another answer making that point/should that comment be an answer? Sometimes there’s something else at work- like sometimes someone will put the same disagreeing comment on every single answer. That's obnoxious so they’ll go.
Comments are for improving a question or answer. If they holistically still seem to have a role to play in that improvement, especially if others agree (via upvotes), they stay.
Also, remember not everyone is on the site every hour of every day. You should absolutely not be flagging useful comments for removal within the initial activity period of a question (usually a couple days to a week, depending). If the post author does, or if the comment has been incorporated, then it's fine, but we don’t want comments with suggestions flagged for removal in less than 24 hours by a third party. These flags should be declined.