### 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 (i == 0 && base_scene_idx >= 0) {
			
			Ref<PackedScene> sdata = props[base_scene_idx];
			ERR_FAIL_COND_V(!sdata.is_valid(), nullptr);
			node = sdata->instantiate(p_edit_state == GEN_EDIT_STATE_DISABLED ? PackedScene::GEN_EDIT_STATE_DISABLED : PackedScene::GEN_EDIT_STATE_INSTANCE); 
			ERR_FAIL_NULL_V(node, nullptr);
			if (p_edit_state != GEN_EDIT_STATE_DISABLED) {
				node->set_scene_inherited_state(sdata->get_state());
			}
		} else if (n.instance >= 0) {
			
			if (n.instance & FLAG_INSTANCE_IS_PLACEHOLDER) {
				String scene_path = props[n.instance & FLAG_MASK];
				if (disable_placeholders) {
					Ref<PackedScene> sdata = ResourceLoader::load(scene_path, "PackedScene");
					ERR_FAIL_COND_V(!sdata.is_valid(), nullptr);
					node = sdata->instantiate(p_edit_state == GEN_EDIT_STATE_DISABLED ? PackedScene::GEN_EDIT_STATE_DISABLED : PackedScene::GEN_EDIT_STATE_INSTANCE);
					ERR_FAIL_NULL_V(node, nullptr);
				} else {
					InstancePlaceholder *ip = memnew(InstancePlaceholder);
					ip->set_instance_path(scene_path);
					node = ip;
				}
				node->set_scene_instance_load_placeholder(true);
			} else {
				Ref<PackedScene> sdata = props[n.instance & FLAG_MASK];
				ERR_FAIL_COND_V(!sdata.is_valid(), nullptr);
				node = sdata->instantiate(p_edit_state == GEN_EDIT_STATE_DISABLED ? PackedScene::GEN_EDIT_STATE_DISABLED : PackedScene::GEN_EDIT_STATE_INSTANCE);
				ERR_FAIL_NULL_V(node, nullptr);
			}