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Exchange Online Directory Synchronization with multiple domains

mtkaiser
mtkaiser used Ask the Experts™
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We are in the process of transitioning from an internally based Exchange system to Exchange Online.  My organization consists of two different companies, each with their own domain.  The hatfield.com domain was the first to move to Exchange Online and it went smoothly.  When I initially signed up for Exchange Online it created a domain of @hatfield.onmicrosoft.com, then I also created @hatfield.com to reflect the email addresses we had already been using.  

The problem started when I tried to do a directory synchronization of mccoy.com.  I created and verified that domain successfully.  However, the directory synchronization is not working correctly.  Rather than creating JDoe@mccoy.com in Exchange Online it created JDoe7925@hatfield.onmicrosoft.com.  

I have contacted Microsoft Support, and they are still trying to figure it out.  Has anyone else seen anything like this before?  Does anyone have any ideas how to resolve this issue?
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Commented:
Have you registered and verified the domain for Mccoy.com in Office 365?

 Basically what you have to do for 1 or 10 domains is make sure they are registered in Office 365 and verified.  Once that is done you need to make sure the User Principal Name matches that domain name.  

Go to ADUC and make sure your users user login (not the pre-2000 ) is user@mccoy.com and not anything else.  If its set to anything else and thats NOT registered in Office 365 is defaults to the onmicrosoft.com Microsoft Logon ID (UPN)

Let me know how that goes.  Also you'll have to remove the users from Office 365 if they've been DirSync'd with a bad UPN.  Changing the UPN in the AD source does NOT change the Microsoft Logon ID.