You may not like my answer. I had to uninstall and reinstall the clients AND the server. I'm still in "testing" with SEP so I have just 40 of 2500 clients running SEP, the other 2460 clients are still running SAVCE. I upgraded the SEPM server from 11.0.5 to 11.0.6 and encountered the same issue you describe. I tried replacing the sylink files manually. I tried by using the sylink replacer utility. I tried uninstall/reinstall the client, all no good. Each client could talk to the server because I used the secars webpage test (
http://service1.symantec.com/SUPPORT/ent-security.nsf/docid/2007101711140148) and it replied with "OK." I finally uninstalled/reinstalled clients and the server and things are running OK now. The client shields have their green dots and the SEPM console clients have their green dots.