Keep in mind there are two separate negative actions that can be taken on a flag:
disputed - This means a 10K+ regular user saw your flag and disagrees with it. He/she cannot leave any messages to you unless it's in a comment. Diamond moderators must still review the flag.
declined - This means a moderator reviewed your flag and found no reason to support it. Moderators can optionally leave a message.
In this case, I'd say it's borderline. I personally despise really short answers, not because they're short, but because they don't explain anything, which sort of makes them fit the requirements of not being an answer but not enough to warrant their removal.
However, in this case, if I were an SO mod, I'd either decline the flag, or at least mark it as helpful and try some editing, then leave you an @ping comment so that both you and the poster can see that the correct course of action is to edit, not flag as not an answer.
Additionally, in the comments, it's clear that you and the answerer are debating the technical merits of the answer. You claim he should talk about X, and he says it doesn't matter in this case. That sounds more like a technical problem with the answer than it being not an answer. If you were only flagging it because of technical issues, then the correct course of action would of course be to decline the flag.
One thing you could do, which would probably work better if you agreed with his answer, is take any information from the comments and edit it into the answer. For instance, take the explanation about the optimizer bypassing the index and place that in the answer.
The other thing I don't like about short answers is that the information that supports the answer ends up spread out in lengthy comments. The answerer, or a skilled editor, should take anything the poster said in the comments and add it to the answer, if it's actually part of the answer.
If you think about it, that's another reason to decline the "not an answer" flag. If the answer can be improved, then it most likely shouldn't be flagged. Moderators should only be flagged when there is no other community recourse or action that a regular user can perform.
So no, don't flag it again, not unless you want another declined flag. Instead, try an edit, or just downvote the answer and move on. :)