Hi,
we use on all SBA the Scom Agent and a Antivirus Solution.
You should exclude Special Folders for the SBA and also for Lync
http://technet.microsoft.com/en-us/library/gg195736.aspx
We have a Special Policy for Windows updates on SBA, because the Installation could stop the SBA Services and the users will logon to our Lync FE.
We don't want this behavior during the business hours and start the updates manually in the Server maintanance time
regards Holger Technical Specialist UC