I don't believe it's new behavior but I'm not 100% sure so I'm positing in this section!
I have 14 layers but only the first three have content in any of the decks, yet I can't seem to be able to remove layers! If I remove layers, when I switch decks, the layers reappear instantly.
Edit: I tried to group the top 10 layers and use the delete group and layers feature but the 10 layers came right back when I switched decks.