I ran into the issue after we migrated our in-house Exchange server to Office 365.
The AD Connect tool is working as designed. The Primary email attribute in the local Active Directory changed, so AD Connect pushed the change to Office 365. To make the correct email address primary, you will need to access the Attribute Editor tab in Active Directory Users and Computers. If you don’t see that tab for your user objects, click on the “View” menu at the top of Active Directory Users and Computers (ADUC) and then click on “Advanced”.*
Then,
- Open the properties of the user object you need to change in ADUC.
Click on the Attributes tab.
Find the proxyAddresses value and click edit.
TYPE IN THE ADDRESS WITH A CAPITAL SMTP (this is what makes it primary)
For example
SMTP: jerry.seinfeld@yaddayadda.com
The change will take effect at next AD Connect Sync (auto or manual).
*note: The Attributes tab won't appear using the Remote Server Administration Tools. You'll need to login to the Domain Controller and use ADUC from there. Alternatively, you can use ADSI Edit remote tools to change the primary email address for a user.
See below for ADSI Edit steps.
Click Start, click Run, type ADSIEdit.msc, and then click OK.
Right-click ADSI Edit, select Connect to, and then click OK to load the domain partition.
In the navigation pane, locate the user object that you want to modify, right-click it, and then click Properties.
In the Attributes list, click the proxyAddresses attribute, and then click Edit.
In the Value to add field, enter the appropriate SMTP address, and then click Add.
Note The primary SMTP address value for the user object should be prepended by an uppercase "SMTP:" designator for it to be formatted correctly for the proxyAddresses attribute.
For example:
"SMTP:username@contoso.com" is an acceptable value.
"username@contoso.com" and "smtp:username@contoso.com" are not acceptable values.
Click OK two times, and then exit ADSI Edit.
The ADSI Edit instructions taken from the TechNet article https://blogs.technet.microsoft.com/hot/2012/06/25/how-to-use-smtp-matching-to-match-on-premises-user-accounts-to-office-365-user-accounts-for-directory-synchronization/