When I implement hybrid mode for an organization, we typically implement Exchange Server 2016 to be the long term hybrid server. This provides the most recent Exchange Server version for management.
Today when I was installing Exchange Server 2016 into an Exchange 2010 organization we started getting directory synchronization errors for some system mailboxes (four of them). This occurred after I ran /PrepareAD, but before the remainder of Exchange Server 2016 was installed.
SystemMailbox{xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx}@XXXXX.com
We only noticed these errors because Office 365 sent an Identity Synchronization Error Report that listed them.
Unable to update this object in Azure Active Directory, because the attribute [Username], is not valid. Update the value in your local directory services.
When I looked in Synchronization Service Manager to see the details in Azure AD Connect, the following errors were there in the export to the Office 365 tenant:
Eventually I found a posting in an MS discussion forum that said to just wait until the install was finished. Apparently /PrepareAD creates the objects, but their configuration is not complete until the rest of Exchange Server 2016 is installed.
Sure enough, after the Exchange Server 2016 install was finished the synchronization errors went away.
Posting in MS discussion forum for reference (see answer from Ytsejamer1):
I did also refresh the connector schema as suggested in this post. However, I did that after running /PrepareAD and before Exchange Server 2016 was installed. I can't say for sure whether this step is required.
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