in the save as dialog there are three options
REUSE, EXCLUDED and REMOVE
all of them do the same at the end and are confusing for the end user
remove and reuse are fine but excluded would be great to behave differently - especially for BOM copies without CAD
If excluded is choosen Windchill should remove these objects from the copy. no reuse, no new parts, just delete them from usage.
This will become more tricky if these BOMs are linked to CAD Assemblies, but since WIndchill is able to drive the structures into CAD as well this should be feasible today.