### 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 state->can_instantiate();
}
Node *PackedScene::instantiate(GenEditState p_edit_state) const {
#ifndef TOOLS_ENABLED
	ERR_FAIL_COND_V_MSG(p_edit_state != GEN_EDIT_STATE_DISABLED, nullptr, "Edit state is only for editors, does not work without tools compiled.");
#endif
	Node *s = state->instantiate((SceneState::GenEditState)p_edit_state);
	if (!s) {
		return nullptr;
	}
	if (p_edit_state != GEN_EDIT_STATE_DISABLED) {
		s->set_scene_instance_state(state);
	}
	if (!is_built_in()) {
		s->set_scene_file_path(get_path());
	}
	s->notification(Node::NOTIFICATION_SCENE_INSTANTIATED);
	return s;
}
void PackedScene::replace_state(Ref<SceneState> p_by) {