Dear Sir:
I have met the same question in OrCAD9.2
After asking the FAE of Cadence, I got the answer:
After you updating the part properties, some parts will have two properties line, one is white, the other is yellow. Save it. After doing this, you need not care the two properties lines. Either create BOM or create netlist, the software use the information in the yellow line only. Maybe this question is a "bug" of OrCAD. As the FAE said, the "bug" is corrected in OrCAD10.
About the importing netlist error, I think you must check the path setup in Allegro, User Preferences-->Config_paths-->devpath, the path is for your PCB Footprint. If Allegro can not find the right footprint in the path, the error is occur!
FYI!