### 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.
} else if (n.type == TYPE_INSTANTIATED) {
			
			if (parent) {
				node = parent->_get_child_by_name(snames[n.name]);
#ifdef DEBUG_ENABLED
				if (!node) {
					WARN_PRINT(String("Node '" + String(ret_nodes[0]->get_path_to(parent)) + "/" + String(snames[n.name]) + "' was modified from inside an instance, but it has vanished.").ascii().get_data());
				}
#endif
			}
		} else {
			
			Object *obj = ClassDB::instantiate(snames[n.type]);
			node = Object::cast_to<Node>(obj);
			if (!node) {
				if (obj) {
					memdelete(obj);
					obj = nullptr;
				}
				if (ResourceLoader::is_creating_missing_resources_if_class_unavailable_enabled()) {
					missing_node = memnew(MissingNode);
					missing_node->set_original_class(snames[n.type]);
					missing_node->set_recording_properties(true);
					node = missing_node;
					obj = missing_node;
				} else {
					WARN_PRINT(vformat("Node %s of type %s cannot be created. A placeholder will be created instead.", snames[n.name], snames[n.type]).ascii().get_data());
					if (n.parent >= 0 && n.parent < nc && ret_nodes[n.parent]) {
						if (Object::cast_to<Control>(ret_nodes[n.parent])) {
							obj = memnew(Control);