The previously reported issue with Cumulative Update 6 (CU6) for Microsoft Exchange Server 2013, that you cannot manage Exchange Online mailboxes by using Exchange Admin Center (EAC) from an on-premises server. This issue has been addressed by Microsoft in lightning response, the following script will help you to fix this issue.

Download: Exchange Online mailboxes cannot be managed in Exchange Server 2013 CU6

To know more about the issue, please see Exchange Online mailboxes cannot be managed by using EAC after you deploy Exchange Server 2013 CU6

-Praveen