### Godot version

v4.1.beta1.official [828ec2c5d]

### System information

Godot v4.1.beta1 - Windows 10.0.23475 - Vulkan (Mobile) - dedicated NVIDIA GeForce RTX 3060 (NVIDIA; 31.0.15.3550) - AMD Ryzen 5 5500 (12 Threads)

### Issue description

I have an exported array for a given type I created with class_name

```
extends Node3D
class_name Enemy
```

It is exported as follow

```
@export var rollable_hazards: Array[Enemy]
```

I populate it using the editor and it works fine, but sometimes it gets emptied after saving the exporting scene. Not sure if it relates with #62916 and/or #77735.

Here's a screen recording I did showing the issue

https://github.com/godotengine/godot/assets/8123916/09d5df4e-83af-4459-b46b-1c62f78c2bb5

Please let me know if you need any additional information.

### Steps to reproduce

1. Export an array from a scene script
2. Populate it with other nodes 
3. Edit the exporting script and save it

### Minimal reproduction project

If you check this branch out, commit [327d03d](https://github.com/lazaromenezes/dungeon-explorer-godot/commit/327d03da6c995ed586b8bc8764bdb051bb42bf7b) was the base for the changes I had into the screen recording.
is_editable_instance = true;
	} else if (p_node->get_owner() && p_owner->is_ancestor_of(p_node->get_owner()) && p_owner->is_editable_instance(p_node->get_owner())) {
		
		is_editable_instance = true;
	}
	NodeData nd;
	nd.name = _nm_get_string(p_node->get_name(), name_map);
	nd.instance = -1; 
	
	if (p_owner->get_scene_inherited_state().is_null() && (p_node == p_owner || (p_node->get_owner() == p_owner && (p_node->get_parent() == p_owner || p_node->get_parent()->get_owner() == p_owner)))) {
		
		nd.index = -1;
	} else if (p_node == p_owner) {
		
		nd.index = -1;
	} else {
		
		nd.index = p_node->get_index();
	}
	
	
	
	
	bool instantiated_by_owner = false;
	Vector<SceneState::PackState> states_stack = PropertyUtils::get_node_states_stack(p_node, p_owner, &instantiated_by_owner);
	if (!p_node->get_scene_file_path().is_empty() && p_node->get_owner() == p_owner && instantiated_by_owner) {
		if (p_node->get_scene_instance_load_placeholder()) {
			
			nd.instance = _vm_get_variant(p_node->get_scene_file_path(), variant_map);
			nd.instance |= FLAG_INSTANCE_IS_PLACEHOLDER;