I just have the same problem. Google-ing for the solution, but I bumped on this topic here. I have the latest version of the game (as of today), just sold duplicates of the books...and ''it's gone''
I am too tired to load savegame from 15 minutes ago, done to much inventory management in that time. My solution: saved game with the name: ''LOST BOOKS'' so I can read them later when I want it to, right from the ''hands'' of the merchant :D