Did this patch do something to the Necromancy of Thay and Dark Amethyst. I've long since found both and opened the book with my main character. I kept the Necromancy of Thay in a separate pouch within my inventory, which I used to carry other quest items to keep things less cluttered, and the book is now back in my inventory and I can't put it back into the pouch. The Dark Amethyst has also appeared in my traveler's chest even though it should be in the book. I didn't know what it was at first since I used it so long ago. I thought maybe it was something I looted and sent to camp by accident since it has the quest colored border, but I couldn't right click it to examine it because there is no right click menu for it.
I don't know if I did something in-game and it was a coincidence that I noticed it after this patch. This may also be related, when I changed locations and went to camp, a bunch of junk (like bones and bed rolls) from the previous location got sucked into the traveler's chest and moved with it.
There is somehing weird going on with putting the book inside containers since Update #4 because it is bound to the character who used it. For me for example when I put it inside a pouch it just straight up vanishes entirely.
So I recommend just keeping it in inventory. Ugly to look at, but there is no risk of it bugging out at least.