### 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.
Node *instantiate(GenEditState p_edit_state) const;
	Ref<SceneState> get_base_scene_state() const;
	void update_instance_resource(String p_path, Ref<PackedScene> p_packed_scene);
	
	int get_node_count() const;
	StringName get_node_type(int p_idx) const;
	StringName get_node_name(int p_idx) const;
	NodePath get_node_path(int p_idx, bool p_for_parent = false) const;
	NodePath get_node_owner_path(int p_idx) const;
	Ref<PackedScene> get_node_instance(int p_idx) const;
	String get_node_instance_placeholder(int p_idx) const;
	bool is_node_instance_placeholder(int p_idx) const;
	Vector<StringName> get_node_groups(int p_idx) const;
	int get_node_index(int p_idx) const;
	int get_node_property_count(int p_idx) const;
	StringName get_node_property_name(int p_idx, int p_prop) const;
	Variant get_node_property_value(int p_idx, int p_prop) const;
	Vector<String> get_node_deferred_nodepath_properties(int p_idx) const;
	int get_connection_count() const;
	NodePath get_connection_source(int p_idx) const;
	StringName get_connection_signal(int p_idx) const;
	NodePath get_connection_target(int p_idx) const;
	StringName get_connection_method(int p_idx) const;
	int get_connection_flags(int p_idx) const;
	int get_connection_unbinds(int p_idx) const;
	Array get_connection_binds(int p_idx) const;
	bool has_connection(const NodePath &p_node_from, const StringName &p_signal, const NodePath &p_node_to, const StringName &p_method, bool p_no_inheritance = false);
	Vector<NodePath> get_editable_instances() const;
	
	int add_name(const StringName &p_name);