Sure, just load your scene and do your changes on an instance of it. Then you can save it back to the disk resource using ResourceSaver.save().
Short example:
var scene_path = "res://my_scene.tscn"
var scene = load(scene_path)
var root = scene.instance()
for node in root.get_children():
node.set_name(new_name)
scene.pack(root)
ResourceSaver.save(scene_path, scene)
Even though the OP didn’t say thanks I’d like to. That’s great help for something I’m facing at present.