And then remember the final scene on the Falcon, where you can clearly see that the books are safely with Rey. She must have taken them before she left, and Yoda knows this.
In that period of time, though, the audience (and Luke) is left to believe that Yoda truly did choose to destroy ancient Jedi artifacts. Which really makes one wonder what the heck is going on—and leaves you to question which side is good, and which is bad? It really blurs the lines between Light and Dark, and crescendos at the throne room scene where Snoke is murdered to when Kylo asks Rey to join him. You almost want her to say yes to his offer! Unlike ESB, the offer isn't just theoretical. Snoke was just overthrown.
In my opinion, the whole sequence was masterfully done.