Some customers have seen where they can end up with a duplicate mailbox within their hybrid environment. This can cause problems when a user, either on premises or in the cloud, has two mailboxes, one on premises and another one in Exchange Online (EXO). The good news is, there is now a work around.
A new parameter that can be called by using the Set-User cmdlet in Exchange PowerShell was introduced recently to help resolve this occasional issue that’s seen when in a hybrid Exchange environment that resulted in duplicate mailboxes.
To set the user Jon, in the Contoso domain, to be a clean object that can be re-licensed without causing the two-mailbox problem, run the command:
Set-User Jon@contoso.com -PermanentlyClearPreviousMailboxInfo
Once you’ve run the command, you can on-board Jon’s on-premises mailbox to the cloud as usual. For additional information you can review this eHelo blog post: https://blogs.technet.microsoft.com/exchange/2018/01/17/permanently-clear-previous-mailbox-info/
However, you do have to remember, that duplicate mailboxes could be a natural and intentional item. Which is why there is logic within EXO to resolve this conflict during the provisioning process. Additional information posted here that explains this shared mailbox concern: https://blogs.technet.microsoft.com/timmcmic/2017/09/17/office-365-fatal-error-recipientnotfoundpermanentexception-has-occurred/
So there you go, two scenarios that can result in a duplicate mailbox, either by error, or by design, and how to fix each given situation.