If you ever wanted to make a game using visibility masking like the classic horror survival game Darkwood, then this demo is for you! In the readme I go over how it works as well as some pitfalls I've found along the way.
If you have any issues or feedback for the demo, please let me know. Thanks!
I've thought about this problem creating a system to save game state. The issue with assigning a UUID works until you have dynamic scenes added to the game at runtime. The nodes in those scenes will all have the same UUID. In the end I ended up just using the paths and saving the fact that the scene that data is being saved for is dynamic. Then the system sees this and re-instances the scene and adds it back to the tree. (A slight adjustment to the path must be made as Godot will create nodes with the at (@) symbol in them, but you can't do that yourself.)
You can see this in action at my demo repo on github.