Two things can help
1) upgrade to 12.1.3 as it seems to be a common issue
http://www.symantec.com/business/support/index?page=content&id=TECH206828
Clients do not update definitions downloaded from Symantec Endpoint Protection Manager
Fix ID: 2715989
Symptom: After the clients come out of standby, the definitions do not update until after Symantec Endpoint Protection Manager restarts.
Solution: Fixed so that LiveUpdate restarts after the client computer recovers from standby.
2)1. Browse to \Program Files\Symantec\Symantec Endpoint Protection Manager\data\outbox\agentinfo
2. Look for any .err files or tmp files & Dat files
3. If you find anything which is not processed by sepm then it might be the reason for the client data loss
4. Stop SEPM services from services.msc
5. Delete all the files inside the location \Program Files\Symantec\Symantec Endpoint Protection Manager\data\inbox\agentinfo
6. Restart the SEPM services.
Check the SEPM now if still issue persist go for step 7
7. Run the Management server configuration wizard.