### 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.
clear();
		ERR_FAIL_V(err);
	}
	err = _parse_connections(scene, scene, name_map, variant_map, node_map, nodepath_map);
	if (err) {
		clear();
		ERR_FAIL_V(err);
	}
	names.resize(name_map.size());
	for (const KeyValue<StringName, int> &E : name_map) {
		names.write[E.value] = E.key;
	}
	variants.resize(variant_map.size());
	for (const KeyValue<Variant, int> &E : variant_map) {
		int idx = E.value;
		variants.write[idx] = E.key;
	}
	node_paths.resize(nodepath_map.size());
	for (const KeyValue<Node *, int> &E : nodepath_map) {
		node_paths.write[E.value] = scene->get_path_to(E.key);
	}
	if (Engine::get_singleton()->is_editor_hint()) {
		
		for (const KeyValue<Node *, int> &E : node_map) {
			node_path_cache[scene->get_path_to(E.key)] = E.value;
		}
	}
	return OK;
}
void SceneState::set_path(const String &p_path) {