You just need to use this!
func change_scene_areas(scene_path):
set_areas_false(get_tree().root);
get_tree.change_scene(scene_path);
#
func set_areas_false(node):
if "monitoring" in node:
node.monitoring = false;
for child in node.get_children():
set_areas_false(child);
Then just call change_scene_areas instead of change_scene. The error is printed when you try and change scenes with Area nodes that have their monitoring property set to true.
You'll also get the same error if you free a Area node when it's monitoring property is true, so if/when you remove Area nodes, you'll want to make sure monitoring is false before calling queue_free.