In some cases, you may encounter an issue where you move a mailbox from Exchange 2003 to Exchange 2010 and, while the move request completed, you receive a warning stating “failed to cleanup the source mailbox after the move.” All of the content is successfully moved, appropriate attributes are updated to point to Exchange 2010, and all new messages are delivered to the Exchange 2010 mailbox. However, you will see disconnected mailboxes for the affected users in Exchange 2003 System Manager and you cannot purge the disconnected mailboxes.
The issue can be caused by search folder problems in the Exchange 2003 mailbox and similar issues were fixed in Exchange 2007 via Service Pack 2. Microsoft describes ways to purge the disconnected Exchange 2003 mailbox at http://support.microsoft.com/default.aspx?scid=kb;EN-US;930363 but the workarounds involve either a number of manual steps or reducing your mailbox retention settings to 0 days and allowing normal Exchange online maintenance to purge the mailboxes. The latter would also purge any legitimately deleted mailboxes that you may want to retain for some period of time so the safest workaround may be to just wait for your normal online maintenance procedures to purge the mailboxes for you (30 days by default).
For more in my series on Exchange 2010 Notes from the Field, please click here.