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I also use custom resources to save but how to you save the custom resources into a file? Do you have to write a parser?

Check out ResourceSaver! Instead of using the "res://" prefix you can persist it to disk with "user://" gdscript.com/solutions/ho... docs.godotengine.org/en/stable/cl...

Unless you mean the ide custom files? In that case you can create a new resource in a folder and set the resource type as your custom one. I do it here (and am even loading all resources in a folder dynamically) github.com/simonsickle/...