Say there is an assembly called "Tool assembly" with lots of parts (so many that fully resolved assembly is unmanageable). I want to design a packaging for it. In order to do that, I save the "Tool assembly" as part with the name "Tool assembly part" with "Preserve geometry references" option turned on. Then I design the packaging, and name it "Packaging assembly".
"Packaging assembly" has the "Tool assembly part" on top in the feature tree, and all other subassemblies, parts and features below it.
Later the "Tool assembly" gets changed. I save it again as part with the name "Tool assembly part renewed". I go to "Packaging assembly" and replace the "Tool assembly part" with "Tool assembly part renewed", and all the entities for mates gets recognized (faces, planes, etc.).
But all the in-reference sketches goes out of context. Is there a way to preserve them?