### 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.
if (ps->has_connection(signal_from, c.signal.get_name(), signal_to, base_callable.get_method())) {
						exists = true;
						break;
					}
				}
				if (common_parent == p_owner) {
					break;
				} else {
					common_parent = common_parent->get_owner();
				}
			}
			if (exists) { 
				continue;
			}
			{
				Node *nl = p_node;
				bool exists2 = false;
				while (nl) {
					if (nl == p_owner) {
						Ref<SceneState> state = nl->get_scene_inherited_state();
						if (state.is_valid()) {
							int from_node = state->find_node_by_path(nl->get_path_to(p_node));
							int to_node = state->find_node_by_path(nl->get_path_to(target));
							if (from_node >= 0 && to_node >= 0) {
								
								if (state->is_connection(from_node, c.signal.get_name(), to_node, base_callable.get_method())) {
									exists2 = true;
									break;
								}
							}