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Go to the Microsoft 365 Admin Center (as an admin) and remove the Business Central license? 
 As the license would still be consumed by the disabled account.
Select the user to remove license.  Click on Licenses and apps and un-check the license.  And Save


Go to BC and disable the user
Once you have removed the BC license from the user in Microsoft Office 365 admin center then go into BC and set the user Status to disabled and remove all permission sets. 
Search for users, select the user and set status to disabled

Keywords: BC Disable users, BC users