This is always a deal breaker for thorough code reviews - it's always super hard to make sure that everything got resolved in a later commit. The only tool I've seen handle this well is SmartBear's Code Collaborator - you mark certain comments as defects, it does a decent job keeping them aligned with their context as revisions happen afterwards, and then you can close them out before marking the review LGTM. Unfortunately, Code Collaborator is horrible at basically everything else. It would be nice to have an easy-to-use todo list that's easy to close out and not lose context.