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The following is a troubleshooting document I provided to my helpdesk staff on this very issue. Perhaps it will help you:
Problem:
The unread count on a mail database or Inbox doesn't appear to match the true number of unread messages in the mailfile.
NOTE: Because Unread counts are USER specific:
Fixes must be applied when signed on as the actual user. They cannot be run by an admin or on the server side.
An Admin can't view the unread count/messages shown to the actual user. (You must shadow the user to observe the problem.)
Possible cause/bug: Deleted or archived a lot of unread emails at once. (There may be other causes.)
Prevention Tip: Mark emails read before deleting large quantities.
Possible Solutions (try in this order, and stop when fixed):
1.In the Inbox/folder with the incorrect count, press the F9 key.
2.In the Inbox/folder with the incorrect count, Edit>Unread Marks>Mark All Read * MARKS EVERYTHING READ *
3.Empty Trash folder
4.Unread documents exist, but user can't find them. Use View>Show>Unread only in the Inbox and the All Documents view to find all unread documents.
5.View indexes are not up to date. Update the index (from any view or folder in the database) by pressing CTRL-SHIFT-F9
6.User can use Edit>Unread Marks>Scan Unread to locate unread documents not showing in any view.
It will search for and display hidden unread documents. Sometimes it will display a hidden view with several of them - mark them each read.
They can also be moved to the appropriate folder at this time.
Repeat until no more unread documents are found.
7.Possibly, user deleted a very large number of documents (+ 300 something) and the unread counter is a bit off.
You can solve this by setting the File>Replication>Replication Settings>Space Savers>'Remove Documents not modified in the last..." to 0 days .
Don't mark the checkbox, though, because you will loose ALL documents.
Feedback response number WEBB87HLVX created by ~Bill Nonweplopobu on 07/19/2010