### 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.
return nodes.size();
}
StringName SceneState::get_node_type(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), StringName());
	if (nodes[p_idx].type == TYPE_INSTANTIATED) {
		return StringName();
	}
	return names[nodes[p_idx].type];
}
StringName SceneState::get_node_name(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), StringName());
	return names[nodes[p_idx].name];
}
int SceneState::get_node_index(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), -1);
	return nodes[p_idx].index;
}
bool SceneState::is_node_instance_placeholder(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), false);
	return nodes[p_idx].instance >= 0 && (nodes[p_idx].instance & FLAG_INSTANCE_IS_PLACEHOLDER);
}
Ref<PackedScene> SceneState::get_node_instance(int p_idx) const {