Whether to retain or remove comments relating to previous versions depends on the nature of the comment. The usual approach is to leave previously published comments in place, because in most cases the comments remain relevant to the way the review was conducted or provides transparency on why changes were made (or not made). But if the comment is clearly no longer applicable (such that a reader would find it confusing or inexplicable) then the comment can be removed, but the contributor may be added to the acknowledgements if appropriate.