This question again passed my view and I just had an idea. I just thought of it and haven't tried it yet, but what if you saved both a JSON and a txt file? The JSON could be a single line which you don't touch, but the txt could include line breaks and be the one you modify. Then when loading it into Godot, you could just check which one is more recent and load that one. Or depending how many keys your JSON files have, you could save each one as a text file, then load them each back in individually, parsing the line breaks to "\n", then setting them to the value of their respective key.
I'll try this and report my results.