You have SEP endpoint clients enrolled, you perform an ATP upgrade, and you modify the ports as directed in the Symantec Advanced Threat Protection 3.0 Release Notes.  ATP Manager shows your endpoints as still enrolled; however, you don't appear to have any communication with those endpoints.

Changing ports disconnects enrolled endpoints from ATP.  But ATP Manager shows them still enrolled.

This is a known issue with ATP.  If you reconfigure the Symantec Endpoint Protection Manager ports, you must re-enroll your Symantec Endpoint Protection endpoints with ATP.