BKE_scene_copy() & co. were pretty much doing nothing right...
Was a tough fight, but at least now they should behave a tad better (and
reported issue is fixed).
Proper fix is to fully rewrite that PoS, it was already a mess without
collections, now it's even hairier to handle properly, we need to use
modern new ID handling API for that (and maybe extend it a bit as
needed). But way too late to do that in 2.80.