### 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.
rconns.push_back(cd.to);
		rconns.push_back(cd.signal);
		rconns.push_back(cd.method);
		rconns.push_back(cd.flags);
		rconns.push_back(cd.binds.size());
		for (int j = 0; j < cd.binds.size(); j++) {
			rconns.push_back(cd.binds[j]);
		}
		rconns.push_back(cd.unbinds);
	}
	d["conns"] = rconns;
	Array rnode_paths;
	rnode_paths.resize(node_paths.size());
	for (int i = 0; i < node_paths.size(); i++) {
		rnode_paths[i] = node_paths[i];
	}
	d["node_paths"] = rnode_paths;
	Array reditable_instances;
	reditable_instances.resize(editable_instances.size());
	for (int i = 0; i < editable_instances.size(); i++) {
		reditable_instances[i] = editable_instances[i];
	}
	d["editable_instances"] = reditable_instances;
	if (base_scene_idx >= 0) {
		d["base_scene"] = base_scene_idx;
	}
	d["version"] = PACKED_SCENE_VERSION;
	return d;
}
int SceneState::get_node_count() const {