Students with unread message in courses that no longer available cannot enter old courses to clear the unread message count. ITS has confirmed with Blackboard that this is a known issue under development — it will be addressed in a future release.
Instructors can only clear unread messages by locating them in the message navigation and then entering the course to mark them as unread. The indication that a course contains unread messages is subtle—it is a line of text underneath the Course Name and Course ID.
Blackboard has always included a course messaging system which allows users to send messages to other course users which remain internal to Blackboard. These messages are not the same as email; course message and email are separate tools but both remain available inside of courses in Syracuse's Blackboard system.
The biggest difference with Blackboard Ultra Navigation is that messages sent in courses are now consolidated and displayed on the main navigation menu. Users will see a badge with a count of unread messages. Clicking on "Messages" will display a list of current courses and organizations where you can click to access the course message or click the plus button to create a new message.
More information about Messages for students and for instructors is available from Blackboard.