I've just duplicated a top-level assembly for re-use in a new project (with some differences). Note that we don't do top-down design, and we make only very limited use of assembly-context referencing, mostly to create things like O-rings that must assemble into a non-circular, milled groove.
My first question was this: What caused By Copy to be greyed out in the Replace dialogue box? Having copied the assembly, I then found I wanted to create a new version of one of the sub-assemblies, but it won't let me use By Copy. I've tried again after quitting and getting an AAX licence, with no change.
So I looked at the Reference Viewer, and it showed about ten children, most of which looked completely unrelated. (After restarting with the AAX licence, it shows just four children). However, if I go to Delete the subassembly, it does not trigger any warnings about other components being deleted; and I can Suppress it with no obvious effect on the rest of the top-level assembly. (It's possible that it was suppressing and resuming that reduced the number of children).
So, does this subassy have children (as shown in the Reference Viewer) or not (as suggested by being able to suppress it)?!?