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I gave myself full access permissions to a number of people's mailboxes to move mail from an old system into their new mailboxes. I went to file>info>account settings and added the other mailboxes manually.

After I was done with it, I went through the same steps to remove the mailboxes manually. However, the folders do not disappear from the Navigation Pane! I've tried right-clicking and deleting the folder; it tells me that I need to remove the mailbox in the 'account settings' options. I go back into 'account settings' and the mailboxes I want to remove are not there. When I try to click the mailbox to view the mail, it tells me that I don't have access to the mailbox (I removed full access permissions when I was done moving the mail).

Am I missing something? How do I remove the mailbox from my Navigation Pane?

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I too have this issue and have been trying to find out why. We recently upgraded to Exchange 2010 and I stopped having the ability to add any user to my navigation pane in Outlook (I am administrator). I have been granting myself full access to a few users to look at other issues. I think I may have found an answer to your question in a Microsoft Technet article which states:

"In Exchange 2010 Service Pack 1 (SP1), Outlook 2007 and Outlook 2010 clients automatically map to any mailbox to which a user has Full Access permissions. If a user is granted Full Access permissions to another user's mailbox or to a shared mailbox, Autodiscover automatically loads all mailboxes to which the user has full access. If the user has full access to a large number of mailboxes, performance issues may occur when starting Outlook. For example, in some Exchange organizations, administrators have full access to all the mailboxes in the organization. In this case, upon starting, Outlook attempts to open all mailboxes in the organization. Users can’t control this behavior and have no way to turn it off."

I don't know how to remedy the situation (yet), but it looks like it explains why some users are "stuck" in the navigation pane.

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