Okay, but what about after the second time? Cause I found the second chest, opened it, and it flew away. Was something supposed to happen, or have I just not found it, or is it not in yet?
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Opening the boxes unlocks some otherwise-hidden content elsewhere! As the game expands, I want to keep including reasons to go back and explore places you might've already been to see what changes; the chests are an early example of that. In this case, the zones to check after opening them are the Hot Springs and the Grove.