So basically you're saying that the cards you want to get rid of your deck are not bad, but that better ones exists in the box. If it is, I'm sorry, but you've picked the wrong game. Building a deck with cards you gather during the adventure is part of the intended gameplay, and nowhere in the game design it is ruled that you'll get access to the cards you want no matter what. Pathfinder ACG is a game about finding stuff, not building the perfect deck from a thousand cards. Games like Magic the Gathering fill that niche, and they're good for that.
But as other have stated before, it is your game, feel free to customize it if you enjoy it more that way. If I were you, I'll just swap the cards of my deck with cards from the box between adventures. Just consider it a house rule. The way you write it in your first post, it feels like you want to twist the rules to use them against themselves.