When Lync Server 2012 shipped, it did not support Server 2012 R2. Naturally since at the time of Lync’s release, Server 2012 R2 had not been released. The UC team’s approach has pretty much always been to test, then support later OSs as appropriate. The late October 2013 Cumulative update (see http://support.microsoft.com/kb/2809243 for details) now supports Server 2012 R2. Yeah!
Like all Lync CU’s you need to do the update carefully and as directed. In a large enterprise, you want to do the updates in such a way as to ensure you maintain service, especially if you are running Enterprise Voice where any downtime, even announced in advance, are not considered a good thing by the users.
In a large enterprise environment, with multiple Front End servers, Lync organise those servers in to upgrade domains, And upgrade domain is, in effect, a set of Front end servers that can be upgraded while the pool remains able to serve users. You upgrade one upgrade domain at a time. This is great as you can upgrade whilst still delivering a service. Of course, if you take several servers out of commission all at once, the pool can function but at a degraded level of performance. So it’s probably best to schedule upgrades at times of light production load to avoid issues with temporary loss of performance.
I’m pleased that this is now supported – I want to re-build my internal lab to use Server 2012 R2 and have Lync integrate with the rest of my testing lab.