In 2017 you have the option to "preserve geometry references" during the save as operation. All internal face IDs are preserved and when you replace the components in your top level assembly, the mates don't fail.
I know this doesn't answer your question, but I thought you'd enjoy knowing that this has been addressed.
Andres, I appreciate the response, although I don't fully understand what you've told me.
You've indicated that, in SWX 2017, a save-as operation on a single-body part would preserve the internal IDs of faces. Does that hold true for edges too? Anything else?
Could you please elaborate on how that affects mate failure during part replacement? I don't understand why preserving internal IDs of one part would make a difference to mate integrity when replacing with a different part.
I believe I misinterpreted what you were trying to accomplish.
It is a common practice, for performance purposes, to save sub-assemblies (already mated) as multibody parts, and then replace those sub-assemblies with the saved multi-body part. Prior to 2017, the internal face IDs (of the sub-assembly) were not preserved, causing mates to fail once it was replaced at the top level assembly.
I haven't tested this yet, but if face IDs of sub-assemblies are being preserved, there is a good chance, that this will also work with single-body and multi-body parts. I believe there is something worth exploring in this enhancement, that could potentially help the scenario that you are presenting.