Outlook 2010 introduced the feature to access and manage multiple exchange accounts within a single Outlook profile. Users with full mailbox permissions can use this feature to manage additional mailboxes in the same way they manage the personal mailbox without switching between different profiles.
Known Limitation with Quest Client Profile Updating Utility (CPUU)
CPUU is unable to update Outlook mail profiles with multiple exchange accounts.
For all limitations of CPUU 5.1 check here:
https://documents.quest.com/qb40605#KnownIssues
Workaround:
Remove the additional exchange accounts and run CPUU again. Add the additional exchange account after the profile update.
Cloudy Migration Life 
Processing of the primary Exchange account in a profile with multiple accounts is now possible with CPUU version 5.4 made possible by the ApprovedExchangeDomains parameter in CPUU.INI