I moved a mailbox from Exchange 2007 to Exchange 2013, everything is fine, but I cannot see the old one disconnected in Exchange 2007 EMC even after a Clean-MailboxDatabase, any ideas why?

can you please run Update-StoreMailboxState on exchange 2013 side and check?

http://www.msexchange.org/kbase/ExchangeServerTips/ExchangeServer2013/ManagementAdministration/clean-mailboxdatabase-exchange-2013.html

Beside the above given reference, when planning to proceed from Exchange 2007 to 2013, I would suggest and refer you on this informative technet blog that covers all the required aspects and would be a good start-up for you to accomplish the job smoothly : http://blogs.technet.com/b/meamcs/archive/2013/07/25/part-1-step-by-step-exchange-2007-to-2013-migration.aspx

To move users mailboxes from Exchange 2007 to 2013, this automated solution (http://www.exchangemigrationtool.com/) could also be a nice approach that provides the option to get this job done without downtime.

I appreciate your responses, but I am not having issues with moving mailboxes. When moving mailboxes from Exchange 2007 to Exchange 2013, it starts making a copy to Exchange 2013 and at the end when completing, it does the cut-over, the mailbox is active on Exchange 2013, and the source mailbox is soft-deleted which means I could still see in Exchange 2007 EMC disconnected mailbox, but I am not.

I didn't this issue when I worked on a migration from 2007 to 2010.