Hello,
It is important to Let you know, if Symantec Endpoint Protection is deleting certain files, then you could check the Logs within the SEP client as below:
1) Start the SEP client Installed
2) Click on View Logs
3) Under Antivirus and AntiSpyware Click on "View Logs" and Click on "Risk Logs."
Do you see any Risk being detected by Symantec Endpoint Protection??
4) Under ProActive Threat Protection Click on "View Logs" and Click on "Threat Logs."
Do you see any Suspicous Threats being detected by Symantec Endpoint Protection??
If yes, please let us know what are those being detected as.
Again, you have installed a older version of Symantec Endpoint Protection on your machine. It is always advisable to use the Latest version of Symantec Endpoint Protection on your machines. The Latest version of Symantec Endpoint Protection is 11.0.7101 and Symantec Endpoint Protection 12.1.1000
About Maintaining Consistency of Software Versions throughout a SEP 11 Organization
http://www.symantec.com/docs/TECH131660
Release notes for Endpoint Protection and Network Access Control 11
Hope that helps!!