It's sad to upvote a comment on a post that's subsequently updated in a way that renders the comment obsolete and not be able flag it afterwards.
There may well be other cases where one would want to flag an upvoted comment too.
- From November '09: Flagging a comment which was upvoted
Note that this was before comment votes could be undone, so one slip and you were stuck. The suggested solution there is to flag the post instead with a note about which comment to look at which is inelegant and potentially a problem as flagging a post can have repercussions beyond just bringing it to the mods' attention.
- From June '10: Flagging a comment which was upvoted
Also pre-comment-upvote-cancelling, which is presumed to address the problem, except that it doesn't in this case.
Update: So here it is nearly three years later and this question lingers unresolved.
It's been positively received (no downvotes yet!), but hasn't gotten any developer response. The problem that this change would address is still a problem. The UI as implemented is still confusing: flags are generally orthogonal to votes on questions and answers, so why do comments take an either/or approach? Comments are purposely second-class citizens, but this seems like privileging them--protection for comments that should be removed!