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.
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.