The item gets some NBT data tacked on to it to ensure the game knows how to change it back. You can use a transformed Tome for crafting, but you probably shouldn't, since you'll lose all other attached items. To transform the tome into another mod's documentation book that is added ...
ouknowhowthesethingsgetstarted,Robbie.Youseeherforthefirsttime.Yourheart skipsandyourfingersbuzz.Can’ttakeyoureyesoffher.Andwhenyoulookathershe knows.Nowaytohideit.Soyoudon’tlook.Useallyourstrengthtonotlook.Butshestill knows.Andanybodyelsearounddoestoo.” ...