### 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_FAIL_COND(!is_inside_tree());
	SceneTree::ProcessGroup *pg = (SceneTree::ProcessGroup *)data.process_group;
	pg->call_queue.push_notification(this, p_notification);
}
void Node::call_thread_safep(const StringName &p_method, const Variant **p_args, int p_argcount, bool p_show_error) {
	if (is_accessible_from_caller_thread()) {
		Callable::CallError ce;
		callp(p_method, p_args, p_argcount, ce);
		if (p_show_error && ce.error != Callable::CallError::CALL_OK) {
			ERR_FAIL_MSG("Error calling method from 'call_threadp': " + Variant::get_call_error_text(this, p_method, p_args, p_argcount, ce) + ".");
		}
	} else {
		call_deferred_thread_groupp(p_method, p_args, p_argcount, p_show_error);
	}
}
void Node::set_thread_safe(const StringName &p_property, const Variant &p_value) {
	if (is_accessible_from_caller_thread()) {
		set(p_property, p_value);
	} else {
		set_deferred_thread_group(p_property, p_value);
	}
}
void Node::notify_thread_safe(int p_notification) {
	if (is_accessible_from_caller_thread()) {
		notification(p_notification);
	} else {
		notify_deferred_thread_group(p_notification);
	}
}
void Node::_bind_methods() {