### 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.
NodePath path;
	};
	Vector<NodeData> nodes;
	struct ConnectionData {
		int from = 0;
		int to = 0;
		int signal = 0;
		int method = 0;
		int flags = 0;
		int unbinds = 0;
		Vector<int> binds;
	};
	Vector<ConnectionData> connections;
	Error _parse_node(Node *p_owner, Node *p_node, int p_parent_idx, HashMap<StringName, int> &name_map, HashMap<Variant, int, VariantHasher, VariantComparator> &variant_map, HashMap<Node *, int> &node_map, HashMap<Node *, int> &nodepath_map);
	Error _parse_connections(Node *p_owner, Node *p_node, HashMap<StringName, int> &name_map, HashMap<Variant, int, VariantHasher, VariantComparator> &variant_map, HashMap<Node *, int> &node_map, HashMap<Node *, int> &nodepath_map);
	String path;
	uint64_t last_modified_time = 0;
	static bool disable_placeholders;
	Vector<String> _get_node_groups(int p_idx) const;
	int _find_base_scene_node_remap_key(int p_idx) const;
#ifdef TOOLS_ENABLED
public:
	typedef void (*InstantiationWarningNotify)(const String &p_warning);
private:
	static InstantiationWarningNotify instantiation_warn_notify;
#endif
protected:
	static void _bind_methods();
public:
	enum {