When I regenerate output products for the System Generator portion of my migrated design in 2013.x, the hierarchy of the project appears to break as the sysgen_project_name_cw.vhd file is no longer produced, why?
This is expected behavior. ISE System Generator needed to reference information from Core Generator and this wrapper file was produced as part of that process. In Vivado System Generator, that is no longer required and so the top level HDL file is now named, sysgen_project_name.vhd.
Modifying the instantiation of the System Generator design in the 2013.x to use the correct instance name will resolve the hierarchy view in the Vivado GUI.