### 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.
node_res->configure_for_local_scene(node, resources_local_to_scene);
											value = node_res;
										}
									} else {
										HashMap<Ref<Resource>, Ref<Resource>>::Iterator E = resources_local_to_scene.find(res);
										Node *base = i == 0 ? node : ret_nodes[0];
										if (E) {
											value = E->value;
										} else {
											if (p_edit_state == GEN_EDIT_STATE_MAIN) {
												
												res->configure_for_local_scene(base, resources_local_to_scene);
												resources_local_to_scene[res] = res;
											} else {
												
												Ref<Resource> local_dupe = res->duplicate_for_local_scene(base, resources_local_to_scene);
												resources_local_to_scene[res] = local_dupe;
												value = local_dupe;
											}
										}
									}
									
								}
							}
						}
						if (value.get_type() == Variant::ARRAY) {
							Array set_array = value;
							bool is_get_valid = false;
							Variant get_value = node->get(snames[nprops[j].name], &is_get_valid);
							if (is_get_valid && get_value.get_type() == Variant::ARRAY) {