### 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 (ccb) {
					binds = ccb->get_binds();
					base_callable = ccb->get_callable();
				}
				CallableCustomUnbind *ccu = dynamic_cast<CallableCustomUnbind *>(c.callable.get_custom());
				if (ccu) {
					unbinds = ccu->get_unbinds();
					base_callable = ccu->get_callable();
				}
			} else {
				base_callable = c.callable;
			}
			
			Node *common_parent = target->find_common_parent_with(p_node);
			ERR_CONTINUE(!common_parent);
			if (common_parent != p_owner && common_parent->get_scene_file_path().is_empty()) {
				common_parent = common_parent->get_owner();
			}
			bool exists = false;
			
			while (common_parent) {
				Ref<SceneState> ps;
				if (common_parent == p_owner) {
					ps = common_parent->get_scene_inherited_state();
				} else {
					ps = common_parent->get_scene_instance_state();
				}
				if (ps.is_valid()) {
					NodePath signal_from = common_parent->get_path_to(p_node);
					NodePath signal_to = common_parent->get_path_to(target);