It would be nice to have a 'Mark all as read' button on Hubski. A thread would go back to unread as soon as a comment is added.
There's a way to, somewhat crudely, emulate it with a 'save' option (it's under the post title). You'll get a notification every time there's a new reply anywhere in the comment tree. I think that what you ask for could be fully done with a browser extension (track what you opened, filter those where comment count hasn't changed since your last visit – nothing hard here), but that's a can of technical worms I'd rather avoid touching myself.