### Godot version

v4.2.dev.custom_build [0ca854232]

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0GB  ram

### Issue description

A node that has a script attached to it and it has a couple of child nodes (type of a child node doesn't matter). In the script you have an export variable of type Node. You save the scene into a file and you add it in level scene. When you start to duplicate that scene in the level and you'll hover over exported variable to show a node path, it will show an incorrect path. 


https://github.com/godotengine/godot/assets/33091666/75088d1b-c014-41e0-bae3-46610eccbad1



### Steps to reproduce

1. create a scene with a node and a child node.
2. attach a script to the parent node and create an export variable of type Node
3. assign child node to that exported variable through the editor
4. save the scene and create a level scene where you are going to add just saved scene.
5. _Possibly requires a reboot of the engine before seeing the bug_
6. start duplicating nodes in the level scene

### Minimal reproduction project

[NodeTest.zip](https://github.com/godotengine/godot/files/12781547/NodeTest.zip)

}
	if (!get_scene_file_path().is_empty()) { //an instance
		node->set_scene_file_path(get_scene_file_path());
		node->data.editable_instance = data.editable_instance;
	}
	StringName script_property_name = CoreStringNames::get_singleton()->_script;
	List<const Node *> hidden_roots;
	List<const Node *> node_tree;
	node_tree.push_front(this);
	if (instantiated) {
		// Since nodes in the instantiated hierarchy won't be duplicated explicitly, we need to make an inventory
		// of all the nodes in the tree of the instantiated scene in order to transfer the values of the properties
		Vector<const Node *> instance_roots;
		instance_roots.push_back(this);
		for (List<const Node *>::Element *N = node_tree.front(); N; N = N->next()) {
			for (int i = 0; i < N->get()->get_child_count(); ++i) {
				Node *descendant = N->get()->get_child(i);
				// Skip nodes not really belonging to the instantiated hierarchy; they'll be processed normally later
				// but remember non-instantiated nodes that are hidden below instantiated ones
				if (!instance_roots.has(descendant->get_owner())) {
					if (descendant->get_parent() && descendant->get_parent() != this && descendant->data.owner != descendant->get_parent()) {
						hidden_roots.push_back(descendant);
					}
					continue;
				}
				node_tree.push_back(descendant);
				if (!descendant->get_scene_file_path().is_empty() && instance_roots.has(descendant->get_owner())) {
					instance_roots.push_back(descendant);
				}
			}