Historical Rules · 18 November 2022
Rule 725.5a
Official source text from the 18 November 2022 Rules release
At the end of a subgame, each nontraditional card not in a supplementary deck that began the subgame in a supplementary deck is turned face down and put on the bottom of that deck. Then each player moves each of their supplementary decks from the subgame command zone to the main-game command zone and shuffles it.