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.