Ok. Restarting Tomcat did fix the unread mail listing for this client, though oddly enough it seems to have created a different problem. Now when I right-click from the Admin UI on an account and select View Mail it does not work. It transfers me to the page
https://myservername/zimbra/auth/ I get an "unable to connect" error.
I will contact the user and see if the duplicate message problem has been corrected as well.