How many Endpoints are duplicated? Kindly check this link, this might help you.
How to repair duplicate IDs on cloned Symantec Endpoint Protection 12.1 clients
http://www.symantec.com/business/support/index?page=content&id=TECH163349&profileURL=https%3A%2F%2Fsymaccount-profile.symantec.com%2FSSO%2Findex.jsp%3FssoID%3D1395884216500815B8bEYdzCUur5vp4hNmLa7v7uoXN6D5jjot
Best Regards,