### 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_COND_V(p_scene_state.is_null(), ERR_INVALID_PARAMETER);
	clear();
	for (const StringName &E : p_scene_state->names) {
		names.append(E);
	}
	for (const Variant &E : p_scene_state->variants) {
		variants.append(E);
	}
	for (const SceneState::NodeData &E : p_scene_state->nodes) {
		nodes.append(E);
	}
	for (const SceneState::ConnectionData &E : p_scene_state->connections) {
		connections.append(E);
	}
	for (KeyValue<NodePath, int> &E : p_scene_state->node_path_cache) {
		node_path_cache.insert(E.key, E.value);
	}
	for (const NodePath &E : p_scene_state->node_paths) {
		node_paths.append(E);
	}
	for (const NodePath &E : p_scene_state->editable_instances) {
		editable_instances.append(E);
	}
	base_scene_idx = p_scene_state->base_scene_idx;
	return OK;
}
Ref<SceneState> SceneState::get_base_scene_state() const {