Also keep in mind, nodes not addressed in VSS but have associations in shader set ups will be disconnected when VSS is synchronized.  This is a normal process, but annoying when you are trying to preserve shader integrity with a new set up.  Scrutinize the original shaders first and decide which nodes are absolutely necessary or are redundunt; clean up you node connections especially if one node is shared among several connectors.  This can confuse VSS and you may not get the intended results you are striving for.