### 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.
GEN_EDIT_STATE_DISABLED,
		GEN_EDIT_STATE_INSTANCE,
		GEN_EDIT_STATE_MAIN,
		GEN_EDIT_STATE_MAIN_INHERITED,
	};
	Error pack(Node *p_scene);
	void clear();
	bool can_instantiate() const;
	Node *instantiate(GenEditState p_edit_state = GEN_EDIT_STATE_DISABLED) const;
	void recreate_state();
	void replace_state(Ref<SceneState> p_by);
	virtual void reload_from_file() override;
	virtual void set_path(const String &p_path, bool p_take_over = false) override;
#ifdef TOOLS_ENABLED
	virtual void set_last_modified_time(uint64_t p_time) override {
		state->set_last_modified_time(p_time);
	}
#endif
	Ref<SceneState> get_state() const;
	PackedScene();
};
VARIANT_ENUM_CAST(PackedScene::GenEditState)
#endif