Step 3 of 5 - Updating shortcuts - has failed with a fatal error.

Ahhhh ok yeah this is a known issue that I've had in my environment as well So when you selected the archive and the destination to move it to, it didnt find the user in question right? And you manually had to select it? If that's the case, you have to start over again and edit the source sites ExchaneMailboxEntry table and change the mbxGUID so that it matches the destination site We have to do this only on a rare occasion, it should be fixed in an upcoming service pack though (not ev9 sp3)