Find out more about our Office 365 C2C Backups
Please follow these steps for setting up permissions for a Mailbox backup.
Use your admin account, which will then have access to all Mailboxes.
You might need to add the "ApplicationImpersonation" role.
Then once you set this up please allow for an hour for the settings to change.
Then you will then see all the Mailboxes within the backup source.