Do you have SEPM 12.1 or 11.x? - have a look here:
Symantec Endpoint Protection 12.1: Best Practices for Disaster Recovery with the Symantec Endpoint Protection Manager
http://www.symantec.com/docs/TECH160736
Symantec Endpoint Protection 11.x: Best Practices for Disaster Recovery with the Symantec Endpoint Protection Manager
http://www.symantec.com/docs/TECH102333
As per notes from the KB:
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The keystore contains the private-public key pair and the self-signed certificate.
During the installation, these files were backed up to the directory that is named \\Program Files\Symantec\Symantec Endpoint Protection Manager\Server Private Key Backup.
You can also back up these files from the Admin panel in the Symantec Endpoint Protection Manager Console.
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Are you able to recover that file from the backup you have?