The rulebook is unclear
on page 13 it says: "put the attached mastery cards into the discard pile"
on page 20 under beginner "when the master'a deck is shuffled for the first time shuffle them into the master's deck"
If they are in the discard pile they will be shuffled anyone, does it mean attached mastery cards, but just does not specify it?
In the Beginner difficulty (page 20) during setup you'll set aside the Mastery cards and only shuffle them into the Master's deck when that deck runs out of cards for the first time. This slows down the Master from leveling up.
Page 13 is talking about what happens when a Master Levels up. Specifically that when you flip the Master over to his higher level, you then put all Mastery cards attached to it into the Master's discard pile.