The directories you see listed (and have access to) in the Azure portal are directories that you (as the identity you use to sign in to the Azure portal) are a member of.
What likely happened is that an administrator of the other Azure AD directory (what you're calling the "Office 365 AD") removed that user account.
If you have access to an administrator user account in the "Office 365 AD", then you can probably restore that user (the easiest path is using the Office 365 portal, though you can also use the Restore-MsolUser cmdlet from the Azure AD PowerShell module.
So, if the account you normally use to sign in to the Azure portal is example@outlook.com, and your "Office 365 AD" is contoso.com, and you have access to a user account admin@contoso.com: Sign in to the Office 365 admin portal (https://portal.office.com) with admin@contoso.com, and restore the deleted user example@outlook.com.
If it has been more than 30 days, the user has been hard-deleted, so you will need to do add example@outlook.com back into contoso.com using the Azure portal. (Again, sign in as admin@contoso.com.)