Hi Russ,
It's sounding to me like you have unintentionally set the library up as a netlist flow. The parts database needs to be defined in the central library and the access database is used purely for parametric data not part mapping. Perhaps you can figure out some tricks to convert things over to a netlist library and then use the migration tool to convert it to a central library (I know this seems like a backwards approach). Not sure how else you can do it without manually creating your parts...
-Travis