### 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.
} while (ss.is_valid());
	return false;
}
Vector<NodePath> SceneState::get_editable_instances() const {
	return editable_instances;
}
int SceneState::add_name(const StringName &p_name) {
	names.push_back(p_name);
	return names.size() - 1;
}
int SceneState::add_value(const Variant &p_value) {
	variants.push_back(p_value);
	return variants.size() - 1;
}
int SceneState::add_node_path(const NodePath &p_path) {
	node_paths.push_back(p_path);
	return (node_paths.size() - 1) | FLAG_ID_IS_PATH;
}
int SceneState::add_node(int p_parent, int p_owner, int p_type, int p_name, int p_instance, int p_index) {
	NodeData nd;
	nd.parent = p_parent;
	nd.owner = p_owner;
	nd.type = p_type;
	nd.name = p_name;
	nd.instance = p_instance;
	nd.index = p_index;
	nodes.push_back(nd);
	return nodes.size() - 1;
}
void SceneState::add_node_property(int p_node, int p_name, int p_value, bool p_deferred_node_path) {