Hi Anthony,
When you add domain which is also a Microsoft Account to Office 365, you cannot login to Outlook.com with the custom domain account. Based on the current situation, you need to remove verified domain in Office 365 and backup your emails first and using such as PST file to import the emails to Office 365. As far as I know, it will just impact email service using an account which both are Microsoft account and Microsoft Online account.
Thanks,
Johnny Zhang