
skizzerz |

In home games, removal of basic/elites is specified in the Adventure Path card. You do not follow organized play rules for removing these cards when playing in a home game.
What I do personally (for OP's question) is if I encounter a card of a higher deck number than the current adventure, I replace it with random cards of that type from the box until I get one of the appropriate number, this way I don't have to spend 15 minutes prepping the box to run lower-level scenarios once I have higher deck cards mixed in. If I'm at the point where I have removed cards, I track which were removed on a sheet of paper and then shuffle all of the removed cards back in the box -- I split them back out afterwards.

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When Runelords was the only AP available, I used to "reset the box" between one gaming group and another. This involved keeping track of which boons had been removed, rebuilding / deconstructing player decks, adding or removing adventure deck cards, etc.
It was a pain in the neck, to be honest.
Now that there are two adventure paths available, I am using a different box for each group. All that setup is too much, to be honest, and cuts in to limited play time fairly significantly. In that regard, Ironvein's solution is less work, if you decide you must run two campaigns from one box. You will still likely need to deconstruct / rebuild player decks between games, but...