There are some issues when using the SharePoint Processing Wizard which is shipped with Quest Migration Manager (not to be confused with a different product called Migration Manager for SharePoint).
What can be done when troubleshooting except just analyzing the log file created by SharePoint Processing Wizard?
Often the issues are of native or environmental character and can be easily reproduced when using native MS tool. Quest SharePoint Processing Wizard offers many advantages like friendly interface etc. It allows processing multiple or all users at the same time and most importantly - it allows to undo and revert changes easily.
But the SharePoint Processing Wizard is using the same API calls the MS tool STSADM is using. If there is an issue, then the first troubleshooting step should be to use Microsoft STSADM command and see if the same issue would occur. The STSADM utility is located by default in this location:
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN
Examples of STSADM usage (Command Line Syntax):
stsadm -o migrateuser -oldlogin <domain\username> -newlogin <domain\username> [-ignoresidhistory]
To determine whether the Stsadm.exe command-line tool was run successfully, please review the Unified Logging Service (ULS) files that are located in the following folder:
C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\LOGS
Note: The log file uses the ServerName-Date-Time.log format.
MS offers excellent instructions on STSADM usage in this article:
http://technet.microsoft.com/en-us/library/cc288981.aspx
For a better understanding of all background procedures, please read also the following article (including the posted comments):
http://www.toddklindt.com/blog/Lists/Posts/Post.aspx?ID=75
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