### 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.
List<Pair<StringName, Variant>> old_state;
						if (node->get_script_instance()) {
							node->get_script_instance()->get_property_state(old_state);
						}
						node->set(snames[nprops[j].name], props[nprops[j].value], &valid);
						
						for (const Pair<StringName, Variant> &E : old_state) {
							node->set(E.first, E.second);
						}
					} else {
						Variant value = props[nprops[j].value];
						if (value.get_type() == Variant::OBJECT) {
							
							Ref<Resource> res = value;
							if (res.is_valid()) {
								if (res->is_local_to_scene()) {
									
									
									
									
									
									
									
									if (n.instance >= 0) {
										Ref<Resource> node_res = node->get(snames[nprops[j].name]);
										if (node_res.is_valid()) {
											node_res->copy_from(res);