My preference would be:
Use a custom flag when all comments on a post are obsolete. If all comments can be deleted, you might as well save your flags by only using one. Moderaters have a tool to purge all comments in a couple of clicks from the post.
Use individual comment flags otherwise. Individual flags are preferred because they're much easier to process directly from the moderator queue without visiting the post (literally one click each).
If you can make all comments on a post obsolete by editing them into the post, that would be ideal.