When certain key "SEP for Mac" files are damaged in the Macintosh directory structure, incorrect information is displayed in the Symantec Endpoint Protection Manager (SEPM) console.  Though communication with the SEPM will continue, management portions of the SEP client GUI may vanish after the Mac is rebooted. Its GUI will then appear as if it is an unmanaged ("self-managed") installation.

Examining the SymantecRegistry.xml and SymantecRegistry.bak files shows that they have been reduced to 0 bytes.

The size of these files can be seen in /Library/Application Support/Symantec/SMC:

….
-rw-r--r-- 1 root staff 1024 Jun 9 11:32:46 2013 SmcState.bak
-rw-r--r-- 1 root staff 6039 Jun 10 10:01:07 2013 SyLink.bak
-rwx------ 1 root staff 6039 Jun 10 10:01:07 2013 SyLink.xml
-rw-r--r-- 1 root staff 6039 Jun 10 10:02:09 2013 SyLinkEx.bak
-rw-r--r-- 1 root staff 0 Jun 9 10:47:10 2013 SymantecRegistry.bak
-rw-r--r-- 1 root wheel 0 Jun 10 11:23:34 2013 SymantecRegistry.xml 
 

This issue is fixed on 12.1 RU5.

Re-installing SEP on the affected computer will restore it to normal operation as a workaround.

Technical Note

When SEP 11 clients are damaged in a similar way, they display an incorrect "12.5.0001.8888" build number.