Z, what you described is exactly how CATIA Assemblies (CATProducts) work, so I don't understand your question. If you do indeed have an instance of the part, then it is just a link to the part, and the assembly should contain the current version of the part when updated.

Are you making your assembly in a CATProduct with the Assembly workbench? (I'm guessing you might be trying to make the assembly as PartBodies within a CATPart with the Part Design workbench)

Please clarify. An attachment of the tree would help.