Hybrid Exchange: Removing an Exchange Online mailbox when both an on-prem and online mailbox exists for the user

In Hybrid Exchange scenarios, if an Active Directory user has been synced to Microsoft 365 without an on-prem mailbox being created first and you assign a Microsoft 365 license to the user, an Exchange Online mailbox will be established. If you come back to On-Prem Exchange Server and create a mailbox, then a mailbox will exist in both locations.

Where you want to remove the Exchange Online mailbox and keep the On-Prem Exchange Server mailbox, follow the below steps.

1. Confirm that the Exchange Online mailbox does not contain content that should be kept.
   
   
2. In Microsoft 365, remove the Exchange Online P1 or P2 license that the user has assigned.
   
   
3. Wait until the Online Mailbox has been soft-deleted for the user. Exchange Admin Center should remove the mailbox from https://admin.exchange.microsoft.com/#/mailboxes 
   
   
4. Confirm that Azure AD Connect has performed a sync and that the user object appears as a Mail Contact in Exchange Online. Exchange Admin Center should display a mail user at https://admin.exchange.microsoft.com/#/contacts
   
   
5. Open Exchange Online PowerShell and connect to you tenancy.
   
   
6. Type the command:
   

   Set-User <user@domain.com> -PermanentlyClearPreviousMailboxInfo

   NOTE: This will permanently remove the Exchange Online mailbox from the service.
   
   
7. Wait a few minutes, then reassign the Exchange Online P1 or P2 license to the user.

For more information, see:

Permanently Clear Previous Mailbox Info
https://techcommunity.microsoft.com/t5/exchange-team-blog/permanently-clear-previous-mailbox-info/ba-p/607619