When flagging comments it is possible to flag comments as either "not constructive" or "obsolete" among other things. If you delete a comment or make an edit that makes another comment obsolete and no longer constructive, I think it is easiest for the moderators if the comment is flagged as obsolete instead of not constructive.
This is correct. However, some users may not see the deleted comments, and know that they are there. Therefore, we may have to tolerate some mismarking.
However, if the comment looks like it's somewhat relevant, it's probably better to mark it "obsolete" than "non-constructive" as a precaution.
I have been interpreting "not constructive" as being more along the lines of destructive criticism. Under that interpretation, anything that was ever constructive would still be constructive, but might become obsolete. I do not know, however, the degree to which others agree with this interpretation.