I have a set of test files with a simple assembly structure.  Assembly ABC.sldasm contains A.sldprt, B.sldprt and C.sldasm.  The assembly C.sldasm contains D.sldprt and E.sldprt.  Parts A and D have drawings.  Assemblies ABC and C also have drawings.  All files are stored in the same folder in the vault.  Everything is checked in.  If I open ABC.sldasm, the EPDM tree looks like this:

All appears to be well.  However, if I attempt to check out the assembly, model A.sldprt and its associated drawing A.slddrw do not appear in the checkout dialog:

Similarly, the contains tab for ABC.sldasm does not show A or its drawing:

In SolidWorks, File...Find References shows A.sldprt:

As does the 'References' button from the File...Open dialog:

The EPDM Copy Tree function, however, shows no sign of A or its drawing:

Yet when I open the copy (which was placed outside the vault), it is pointing back to the original in the vault:

I am convinced that EPDM 2016 has one or more fundamental flaws with reference management that were not present in 2015.  I have been using this same set of test files for 4 years with no problems until EPDM 2016.  This is the second odd behavior I have noted.  The first can be found here​.