Ok so we all know they go into the treehouse and they say they can't take anything out of the box until they found D.B.'s treasure. They made an oath on it even. Later in the movie I can't remember when, It could have been after the waterfall scene. Seth Green's Character pulls out the little toy action figure that was shown inside the forbidden box earlier in the film and says something in a mimicing voice.
It was all put back in the box, but they then obviously took what was inside the box with them (looked like Dan was carrying them around in his pouch along with his first aid kit). This is clearly shown whey they're driving to their destination and pop in their mixtape (the one with their DJ intros) to listen to. Also when Jerry uses the Indiana Jones compass. And then at the end, when they find D.B's skeleton, they each toss their "precious treasures" away.
What Jerry meant was that they couldn't take what they put in the box OFFICIALLY back until they found D.B's treasure. That's all. He didn't meant it to be taken as literal as you seem to have.
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