It will make the changes in the sylink file...
.....Edit....
Compare both these sylink files.
In SEPM every group has its own sylink and Group ID
Program Files\Symantec:\Symantec Endpoint Protection Manager\data\outbox\agent\0F4C825779F74C7000A2E19EBC385AA7 --(the first 4 digit represent the group id)
symantec endpoint protection\sylink.xml --on the clent.
One more thing to do Open the SEP Clients-- Help and Support -Troubleshooting -check the policy serial number ( 4 digits)
Then check if you have a folder in the above location on sepm server starting with that number..
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You can check the policy serial number in client and server... If both are same then it has taken the proper settings form the server...