Written books seem to have a "resolved" NBT tag when they get opened for the first time. This tag prevents opened written books from stacking with otherwise identical unopened ones, and it appears as an NBT tag in F3+H mode, but /clear commands cannot detect it (when acquiring a hacked written book using /give and putting in the "resolved" tag, /clear detects it perfectly). commands detect it fine. Turns out I wasn't casting properly.

How to reproduce:
1. Create a new creative world (make sure you're in F3+H mode)
2. Make a written book
3. Open your inventory and use pick block to clone the book
4. Open one of the books
5. Hover over the books in the inventory. One stack will have one more NBT tag than the other.