### 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.
if (name_map.has(p_string)) {
		return name_map[p_string];
	}
	int idx = name_map.size();
	name_map[p_string] = idx;
	return idx;
}
static int _vm_get_variant(const Variant &p_variant, HashMap<Variant, int, VariantHasher, VariantComparator> &variant_map) {
	if (variant_map.has(p_variant)) {
		return variant_map[p_variant];
	}
	int idx = variant_map.size();
	variant_map[p_variant] = idx;
	return idx;
}
Error SceneState::_parse_node(Node *p_owner, Node *p_node, int p_parent_idx, HashMap<StringName, int> &name_map, HashMap<Variant, int, VariantHasher, VariantComparator> &variant_map, HashMap<Node *, int> &node_map, HashMap<Node *, int> &nodepath_map) {
	
	
	
	
	
	if (p_node != p_owner && p_node->get_owner() != p_owner && !p_owner->is_editable_instance(p_node->get_owner())) {
		return OK;
	}
	bool is_editable_instance = false;
	
	
	if (p_node != p_owner && !p_node->get_scene_file_path().is_empty() && p_owner->is_editable_instance(p_node)) {
		editable_instances.push_back(p_owner->get_path_to(p_node));