I'm not sure if you have fixed this, but I can't find any mention of it in the few patch notes I could find nor on the UESP.
In short: The big bookshelf on the 1st floor of the library in Lakeview manor bugs out when you interact with a certain row of the shelf and causes the books to disappear. So far it seems to happen on the second lowest row of the shelf.
Mods installed: None, it's a completely Vanilla save.
I've attached the save file, where you spawn inside the manor. You only have to take a few steps toward the library and interact with the shelf.