### 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.
}
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		Node *c = p_node->get_child(i);
		Error err = _parse_connections(p_owner, c, name_map, variant_map, node_map, nodepath_map);
		if (err) {
			return err;
		}
	}
	return OK;
}
Error SceneState::pack(Node *p_scene) {
	ERR_FAIL_NULL_V(p_scene, ERR_INVALID_PARAMETER);
	clear();
	Node *scene = p_scene;
	HashMap<StringName, int> name_map;
	HashMap<Variant, int, VariantHasher, VariantComparator> variant_map;
	HashMap<Node *, int> node_map;
	HashMap<Node *, int> nodepath_map;
	
	if (scene->get_scene_inherited_state().is_valid()) {
		String scene_path = scene->get_scene_inherited_state()->get_path();
		Ref<PackedScene> instance = ResourceLoader::load(scene_path);
		if (instance.is_valid()) {
			base_scene_idx = _vm_get_variant(instance, variant_map);
		}
	}
	
	Error err = _parse_node(scene, scene, -1, name_map, variant_map, node_map, nodepath_map);
	if (err) {