1. If you have replaced a reference using ReplaceReference Method (IswDMDocument), then GetExternalFeatureReferences (SwDMDocument15) does not return the new reference.  It returns the old references but SolidWorks Explorer and the SolidWorks Application return the right set of references.  Here is the an example:

Original References using SolidWorks Explorer (click on picture to enlarge):

I then used  ReplaceReference Method (IswDMDocument) in the Document Manager.  The screenshot below shows that the SolidWorks Explorer recognizes the change (click on picture to enlarge):

Now a call to GetExternalFeatureReferences (SwDMDocument15) returns an in correct list of references.  02997.sldasm is the old reference.  00839.sldasm is the new reference  (click on picture to enlarge).

  2.  GetExternalFeatureReferences (SwDMDocument15) returns nothing for drawings or parts with In-context references.  Again here is an example.

03500.sldprt has an In-Context Reference to 03544.sldasm as seen in SolidWorks explorer:

When I call GetExternalFeatureReferences (SwDMDocument15), I get no output of references:

Current Conclusions:  Don't use GetExternalFeatureReferences Method (IswDMDocument15) until SolidWorks fixes it because it is broken.  It returns incorrect informaiton.