### 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)

PackedStringArray warnings = get_configuration_warnings();
	String all_warnings;
	for (int i = 0; i < warnings.size(); i++) {
		if (i > 0) {
			all_warnings += "\n\n";
		}
		// Format as a bullet point list to make multiple warnings easier to distinguish
		// from each other.
		all_warnings += String::utf8("•  ") + warnings[i];
	}
	return all_warnings;
}
void Node::update_configuration_warnings() {
	ERR_THREAD_GUARD
#ifdef TOOLS_ENABLED
	if (!is_inside_tree()) {
		return;
	}
	if (get_tree()->get_edited_scene_root() && (get_tree()->get_edited_scene_root() == this || get_tree()->get_edited_scene_root()->is_ancestor_of(this))) {
		get_tree()->emit_signal(SceneStringNames::get_singleton()->node_configuration_warning_changed, this);
	}
#endif
}
bool Node::is_owned_by_parent() const {