Have you figured this out? I have made some progress doing the same thing, but not perfect yet.
I have a piece I cut on a waterjet that I would take my mill for a final operation. I created a CAD file of the rough waterjet part, and another of the finished part after milling. I imported both models, one as the part and one as the workpiece.
Seemed to work great. I no longer had the block around the part. The workpiece was the model I imported. Before I did this I had unnecessary tool paths cutting air instead of being limited to the actual workpiece.
The simulation is odd, however. It shows material underneath the workpiece. The top contour is correct, it is the workpiece I imported, but the bottom is not.
Close, but not quite right yet. Suggestions would be appreciated.