### 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.
ERR_FAIL_INDEX_V(p_idx, nodes.size(), Ref<PackedScene>());
	if (nodes[p_idx].instance >= 0) {
		if (nodes[p_idx].instance & FLAG_INSTANCE_IS_PLACEHOLDER) {
			return Ref<PackedScene>();
		} else {
			return variants[nodes[p_idx].instance & FLAG_MASK];
		}
	} else if (nodes[p_idx].parent < 0 || nodes[p_idx].parent == NO_PARENT_SAVED) {
		if (base_scene_idx >= 0) {
			return variants[base_scene_idx];
		}
	}
	return Ref<PackedScene>();
}
String SceneState::get_node_instance_placeholder(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), String());
	if (nodes[p_idx].instance >= 0 && (nodes[p_idx].instance & FLAG_INSTANCE_IS_PLACEHOLDER)) {
		return variants[nodes[p_idx].instance & FLAG_MASK];
	}
	return String();
}
Vector<StringName> SceneState::get_node_groups(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), Vector<StringName>());
	Vector<StringName> groups;
	for (int i = 0; i < nodes[p_idx].groups.size(); i++) {
		groups.push_back(names[nodes[p_idx].groups[i]]);
	}
	return groups;
}
NodePath SceneState::get_node_path(int p_idx, bool p_for_parent) const {