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 .
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.