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I store all the collectables that have been picked up (puzzle pieces, keys, blobs), the checkpoints that have been activated and the current checkpoint, and every time a new checkpoint is activated or a collectable is picked up, I save that information to a file using JSON.

Next time the game is run, I load the information and update the map accordingly, removing collectables and activating checkpoints, and spawning the player at the current checkpoint.

There's a great tutorial page in the Godot docs about saving games, I recommend you check that out for more details: https://docs.godotengine.org/en/stable/tutorials/io/saving_games.html