### 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.
FLAG_ID_IS_PATH = (1 << 30),
		TYPE_INSTANTIATED = 0x7FFFFFFF,
		FLAG_INSTANCE_IS_PLACEHOLDER = (1 << 30),
		FLAG_PATH_PROPERTY_IS_NODE = (1 << 30),
		FLAG_PROP_NAME_MASK = FLAG_PATH_PROPERTY_IS_NODE - 1,
		FLAG_MASK = (1 << 24) - 1,
	};
	enum GenEditState {
		GEN_EDIT_STATE_DISABLED,
		GEN_EDIT_STATE_INSTANCE,
		GEN_EDIT_STATE_MAIN,
		GEN_EDIT_STATE_MAIN_INHERITED,
	};
	struct PackState {
		Ref<SceneState> state;
		int node = -1;
	};
	static void set_disable_placeholders(bool p_disable);
	int find_node_by_path(const NodePath &p_node) const;
	Variant get_property_value(int p_node, const StringName &p_property, bool &found) const;
	bool is_node_in_group(int p_node, const StringName &p_group) const;
	bool is_connection(int p_node, const StringName &p_signal, int p_to_node, const StringName &p_to_method) const;
	void set_bundled_scene(const Dictionary &p_dictionary);
	Dictionary get_bundled_scene() const;
	Error pack(Node *p_scene);
	void set_path(const String &p_path);
	String get_path() const;
	void clear();
	Error copy_from(const Ref<SceneState> &p_scene_state);
	bool can_instantiate() const;