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The Reference Manager will repath Xrefs across multiple files and/or folders. It's optionally installed with Civil 3D, and can be found in the Start/Autodesk/Autodesk AutoCAD Civil 3D XXXX folder.
What we've done to deal with the name issue is change the Reference Name of each of the Xrefs in our template to something generic (EX = existing, PR = Proposed). We can then repath those Xrefs to any existing or proposed file, regardless of file name, and it will hold any default properties we have set (layer overrides, basepoint, scale, etc.).