### 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.
Array get_array = get_value;
								if (!set_array.is_same_typed(get_array)) {
									value = Array(set_array, get_array.get_typed_builtin(), get_array.get_typed_class_name(), get_array.get_typed_script());
								}
							}
						}
						if (p_edit_state == GEN_EDIT_STATE_INSTANCE && value.get_type() != Variant::OBJECT) {
							value = value.duplicate(true); 
						}
						bool set_valid = true;
						if (ResourceLoader::is_creating_missing_resources_if_class_unavailable_enabled() && value.get_type() == Variant::OBJECT) {
							Ref<MissingResource> mr = value;
							if (mr.is_valid()) {
								missing_resource_properties[snames[nprops[j].name]] = mr;
								set_valid = false;
							}
						}
						if (set_valid) {
							node->set(snames[nprops[j].name], value, &valid);
						}
					}
				}
				if (!missing_resource_properties.is_empty()) {
					node->set_meta(META_MISSING_RESOURCES, missing_resource_properties);
				}
			}
			
			
			for (int j = 0; j < n.groups.size(); j++) {
				ERR_FAIL_INDEX_V(n.groups[j], sname_count, nullptr);