Nadya's Codex is a special codex created by a Grand Coven witch by the name of Nadya. Nadya was a gifted witch who had a knack for cracking coded texts, however Nadya was also selfish, once she cracked a code she then coded its secrets for herself, making the codex damn near indecipherable to anyone else.
Nadya was hunted down by the Men of Letters, and had her life's work -- including the codex taken away. When Cuthbert Sinclair found out about the codex, he implemented a plan in secret to make sure that the Grand Coven could never get their hands on the book again by creating the Werther Box. It's in the Werther Box the codex remained until Sam Winchester came looking for it and was able to retrieve it.