Jim,
Like Russ, I have had to redirect the cross-references manually following conversion; HOWEVER, I have also noticed that existing IDs in the unstructured version seem to get put into the converted element as an attribute. In other words, if my EDD defines a Title element with an Id attribute and the unstructured document contains a title paragraph that is the target of a cross-reference, then upon conversion the corresponding Title element has TWO attributes, one is named Id and the other ID. Id has no value, but ID does. The structured document does not validate and I have to delete the ID attribute to make it validate.
This leads me to believe that had I named the attribute ID in my EDD, then it would be assigned a value upon conversion; however, I have never tried this. If I had, FrameMaker would likely create the Title element with two attributes, both named ID!!!
Take it for what it is worth,
Van