### 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.
}
						nl = nullptr;
					} else {
						if (!nl->get_scene_file_path().is_empty()) {
							
							Ref<SceneState> state = nl->get_scene_instance_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;
									}
								}
							}
						}
						nl = nl->get_owner();
					}
				}
				if (exists2) {
					continue;
				}
			}
			int src_id;
			if (node_map.has(p_node)) {
				src_id = node_map[p_node];
			} else {
				if (nodepath_map.has(p_node)) {