### 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.
return nodes.size() > 0;
}
static Array _sanitize_node_pinned_properties(Node *p_node) {
	Array pinned = p_node->get_meta("_edit_pinned_properties_", Array());
	if (pinned.is_empty()) {
		return Array();
	}
	HashSet<StringName> storable_properties;
	p_node->get_storable_properties(storable_properties);
	int i = 0;
	do {
		if (storable_properties.has(pinned[i])) {
			i++;
		} else {
			pinned.remove_at(i);
		}
	} while (i < pinned.size());
	if (pinned.is_empty()) {
		p_node->remove_meta("_edit_pinned_properties_");
	}
	return pinned;
}
Node *SceneState::instantiate(GenEditState p_edit_state) const {