Civil File Manager SS10 to ORD Conversion - Element dependencies to reference file elements are broken on conversion

We have been tasked with converting an SS10 project to ORD.  Some of our SS10 civil files contain linear elements that were created using offset elements from an alignment reference file.  When these SS10 files are converted through Civil File Manager, the dependencies to the reference file elements no longer appear.  Civil File Manager is locating and converting the attached reference files as they are in the same folder.

Is maintaining these dependencies beyond what CFM can do, or are we organizing/performing our conversion incorrectly?