Hi James,
In a hybrid environment, it’s recommended to create users in the on-premises AD server, then sync them to Office 365 via DirSync. In this way, all the exchange attributes related to the on-premises mailboxes will also be synced. If the user is created in Office 365 Portal, even though we can soft match the user with the AD user via DirSync, but it will cause potential issues.
For best practices, deleting the user in Office 365 and re-syncing the user to Office 365 is recommended. I suggest you back up all the data files used in OneDrive for Business, then restore them after the user is re-created. Sorry for any inconvenience caused by the issue.