vSphere Replication 6.1.1
is this the VR release that you are using? I couldn't locate release notes for the same on vmware website.
if you are using vSphere Replication to replicate your VMs, it's quite simple to include or not to include one of the vDisk from being replicated. So if you attach an additional vDisk to your fileserver VM and you don't want it to be replicated, just edit vSphere replication for that VM and deselect that vDisk which you don't want to replicate.
As of today, there is no vSphere Replcation version 6.1.1.
The latest version from the 6.x code line is 188.8.131.52 from May 2015.