### 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.
Ref<SceneState> ss = this;
	do {
		for (int i = 0; i < ss->connections.size(); i++) {
			const ConnectionData &c = ss->connections[i];
			NodePath np_from;
			if (c.from & FLAG_ID_IS_PATH) {
				np_from = ss->node_paths[c.from & FLAG_MASK];
			} else {
				np_from = ss->get_node_path(c.from);
			}
			NodePath np_to;
			if (c.to & FLAG_ID_IS_PATH) {
				np_to = ss->node_paths[c.to & FLAG_MASK];
			} else {
				np_to = ss->get_node_path(c.to);
			}
			StringName sn_signal = ss->names[c.signal];
			StringName sn_method = ss->names[c.method];
			if (np_from == p_node_from && sn_signal == p_signal && np_to == p_node_to && sn_method == p_method) {
				return true;
			}
		}
		if (p_no_inheritance) {
			break;
		}
		ss = ss->get_base_scene_state();