Users have two mailboxes, one online and one on-premise

While working with an Exchange hybrid environment (Exchange 2016 on-premise and Exchange Online) it became apparent that some users had two mailboxes; one on-premise and one in Exchange Online.  Their primary mailbox was in the on-premise environment, the one online was empty and unused.

There are several issues with this.  Firstly, it will cause issues with migration when the time comes – how can a user have 2 mailboxes?  Secondly, other Office 365 services were using the wrong mailbox (for example, Teams was showing an empty calendar for these users as it was not looking at the one-premise mailbox).

I had a support case open with Microsoft for over 3 months and they couldn’t resolve it without completely deleting the user account in Office 365.  If it was a new user that wouldn’t be a problem, but these users have been around for years and have so much data in Teams, SharePoint, Dynamics, etc – that would have been a huge admin overhead to restore.

Eventually I came across a PowerShell command that solved the issue by permanently removing all Exchange Online data.  These are the steps I took to resolve it, but proceed with caution as you need to understand whether the users have anything of any value in Exchange Online:

1. Disable the Exchange Online license for the affected user
2. Run the following PowerShell cmdlet once connected to Exchange Online PowerShell:

   Set-User user@ourdomain.com -PermanentlyClearPreviousMailboxInfo

3. Wait for the on-premise AD to sync with Azure AD or force a sync on the server running AADC:

   Start-ADSyncSyncCycle -PolicyType Delta

4. Enable the Exchange Online license for the user

Now the user only has one mailbox, enabling the license does not create a second mailbox.