Sorry I took some time to answer.
I think it's fine to overwrite existing files as long as it's simple for the user to select them. I'm working on something to bring up a file selector from a GraphNode, I'll let you know when it's ready

So, I've added a new option to display a file dialog from a graph node

All you have to do is to pass these options when calling set_input with a string type.

var opts = {
	"file_dialog": {
		"mode": FileDialog.MODE_SAVE_FILE,
		"filters": ["*.scn", "*.tscn"]
	}
}
set_input(0, "File", ConceptGraphDataType.STRING, opts)

And I see you fixed your issue on the file override, good job!

Pretty nice stuff on the file chooser! Good job!