Unfortunately, there isn't. Facebook tracks all articles based on the URL of the page the comment box is displayed on. JFBConnect will try to determine the best 'final' destination URL for an article. That allows for the comment box to be displayed on a blog layout and the box will still be for the destination URL. However, if you changed the category or menu structure, it's likely that the final URL for the article has changed. In that case, there's not anything JFBConnect can do automatically. You could choose to set the comment tag on each article with the 'old' URL, but you'd be required to setup the redirects from the old URL to the new URL and verify things work as expected.
I hope that helps explain, but should you need anything else, just let us know.
Thanks,
Alex