You could store the changes to a temporary savefile that you delete once the player exits the game - or copy into the regular savefile, when the player saves manually.
Click here for an introduction on how to save games in Godot.
While setting this stuff up can be a lot of work, I'd argue it's worth the effort, especially when your game gets bigger and memory use becomes a more important factor. It's also worth pointing out that this gives you a lot of control about what to load and when.