### 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)

ERR_THREAD_GUARD_V(nullptr);
	Node *node = nullptr;
	bool instantiated = false;
	if (Object::cast_to<InstancePlaceholder>(this)) {
		const InstancePlaceholder *ip = Object::cast_to<const InstancePlaceholder>(this);
		InstancePlaceholder *nip = memnew(InstancePlaceholder);
		nip->set_instance_path(ip->get_instance_path());
		node = nip;
	} else if ((p_flags & DUPLICATE_USE_INSTANTIATION) && !get_scene_file_path().is_empty()) {
		Ref<PackedScene> res = ResourceLoader::load(get_scene_file_path());
		ERR_FAIL_COND_V(res.is_null(), nullptr);
		PackedScene::GenEditState edit_state = PackedScene::GEN_EDIT_STATE_DISABLED;
#ifdef TOOLS_ENABLED
		if (p_flags & DUPLICATE_FROM_EDITOR) {
			edit_state = PackedScene::GEN_EDIT_STATE_INSTANCE;
		}
#endif
		node = res->instantiate(edit_state);
		ERR_FAIL_NULL_V(node, nullptr);
		node->set_scene_instance_load_placeholder(get_scene_instance_load_placeholder());
		instantiated = true;
	} else {
		Object *obj = ClassDB::instantiate(get_class());
		ERR_FAIL_NULL_V(obj, nullptr);
		node = Object::cast_to<Node>(obj);
		if (!node) {
			memdelete(obj);
		}
		ERR_FAIL_NULL_V(node, nullptr);