Disqus uses universal identifiers to uniquely specify each post. The add-on should be configured to use the same identifiers that were present in the Disqus WP add-on when I first used it -- my old WP comments transferred directly over. However, there is a chance this could have changed, and it would not be possible for the add-on to know that the Disqus add-on was using a different format.

Last I checked, I don't have a way to determine the identifiers Disqus is using for existing content. If you contact the Disqus help support, I'll be glad to help do whatever I can to make sure the two are in sync. Otherwise they may have something on their end they could do to link the posts.