Problem: Minecraft saves (and sometimes renders) block entities after they've been destroyed, until the game is quit and reopened.
Steps to reproduce:
1. Run a command filling a large area (I used 1000+ blocks) with enchanting tables
2. Run a command fill the same area with air.
3. Run a command fill the same area with chests.
The chests themselves won't render because they would be more than double chests, but Minecraft will render the books from on top of the enchanting tables. You could also switch steps 1 and 3 to render the chests inside the enchanting tables.
What this means is that Minecraft is using storage to save the past locations of all tile entities, even after they are destroyed.