I don't know about mirrored assemblies, but I had a similar problem with "Save bodies". I accidently checked "Copy custom properties to new parts". Unchecking didn't break the link. What did work after un-checking, delete out all the custom properties in the parent part and regen the child. You should see the custom properties links broken now. When you re-create custom properties in the parent part, they don't copy to the child (as expected).
Same problem here. Any better solutions found?
Open a new, empty assembly template and inport your mirrored assembly there. Select "Dissolve Subassembly" and you are ok again!