This behavior sounds like it would be happening due to the initialization of the installer. You may want to schedule your patch deployment for a time when users will not be using their machines. Have you contacted Microsoft or checked any of their forums for known issues with install of Lync updates?
Thanks adamg23, I am aware that the initialization of the installer will close Lync (http://social.technet.microsoft.com/Forums/lync/en-US/5bbc1de5-3da9-498b-9bb0-70d4a6eb15c1/lync-client-closes-when-applying-updates?forum=ocsclients)
What is the most effective way to install Lync patches using Shavlik agents (without impacting the user/closing Lync)?
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Since there's not really any way we can control this behavior during patching it would be best to try to schedule your patch deployment at a time that users will not be using their machines.
Most patches will not apply when the application to be updated is still open/running. It's just that the users see more difference here since they are using Lync.
If you can't set up a schedule to have the install run later at night or early in the morning before users are on the machines, you could at least enable a remote dialog to make them aware that apps will close and updates are being applied. The setting for this can be found on the General tab when creating/editing a custom patch deployment template.
I hope that helps.
Thanks again for the recommendations. With our current agent policy, patches are deployed during the business day while laptops are connected to the network. It appears that deploying patches at restart or at start up is not an option.