O365 sync won’t assign a mailbox to use when 2 users have the same PrimarysmtpAddress and different UPNs. Go to System Configuration > Office 365 Module to specify a preferred domain to be used for an O365 sync when addresses are unclear. Enter the preferred domain in the field called “Preferred domain for ambiguous user match results”.

Or, manually set a preferred domain using this PowerShell command:

Set-ASConfiguration¬†-SettingDefinition¬†Office365PreferredDomainForUserMatch¬†“yourdomain”

Now, the preferred domain is used when you run an O365 sync.

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