### 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.
GDCLASS(SceneState, RefCounted);
	Vector<StringName> names;
	Vector<Variant> variants;
	Vector<NodePath> node_paths;
	Vector<NodePath> editable_instances;
	mutable HashMap<NodePath, int> node_path_cache;
	mutable HashMap<int, int> base_scene_node_remap;
	int base_scene_idx = -1;
	enum {
		NO_PARENT_SAVED = 0x7FFFFFFF,
		NAME_INDEX_BITS = 18,
		NAME_MASK = (1 << NAME_INDEX_BITS) - 1,
	};
	struct NodeData {
		int parent = 0;
		int owner = 0;
		int type = 0;
		int name = 0;
		int instance = 0;
		int index = 0;
		struct Property {
			int name = 0;
			int value = 0;
		};
		Vector<Property> properties;
		Vector<int> groups;
	};
	struct DeferredNodePathProperties {
		Node *base = nullptr;
		StringName property;