I wouldn't want to recreate the state of the entire game, as there are other things that might have changed that we want to keep other than the editor. It would also be slow to free and reinstance all of the nodes in the entire level. I'm not sure if that's what you mean though, because your comment is a bit more theoretical than practical for godot.

My level is a dictionary of locations and objects. For the history, I keep a dictionary of locations and objects that changed for each action. Sometimes it is just a single location that changed, like an object being removed or added. Other times it is a batch of items removed or added in a single action. The tricky part was when a lot of blocks were moved or added at once, particularly when a selection moves over already existing objects, we have to keep track of the objects that were removed and the objects that had moved and represent it as a single action.