### 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->add_to_group(snames[n.groups[j]], true);
			}
			if (n.instance >= 0 || n.type != TYPE_INSTANTIATED || i == 0) {
				
				if (i > 0) {
					if (parent) {
						bool pending_add = true;
#ifdef TOOLS_ENABLED
						if (Engine::get_singleton()->is_editor_hint()) {
							Node *existing = parent->_get_child_by_name(snames[n.name]);
							if (existing) {
								
								
								
								
								
								
								
								
								if (instantiation_warn_notify) {
									instantiation_warn_notify(vformat(
											TTR("An incoming node's name clashes with %s already in the scene (presumably, from a more nested instance).\nThe less nested node will be renamed. Please fix and re-save the scene."),
											ret_nodes[0]->get_path_to(existing)));
								}
								node->set_name(snames[n.name]);
								parent->add_child(node, true);
								pending_add = false;
							}
						}
#endif