### 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 NodePath(".");
	}
	return NodePath(sub_path, false);
}
int SceneState::get_node_property_count(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), -1);
	return nodes[p_idx].properties.size();
}
StringName SceneState::get_node_property_name(int p_idx, int p_prop) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), StringName());
	ERR_FAIL_INDEX_V(p_prop, nodes[p_idx].properties.size(), StringName());
	return names[nodes[p_idx].properties[p_prop].name & FLAG_PROP_NAME_MASK];
}
Vector<String> SceneState::get_node_deferred_nodepath_properties(int p_idx) const {
	Vector<String> ret;
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), ret);
	for (int i = 0; i < nodes[p_idx].properties.size(); i++) {
		uint32_t idx = nodes[p_idx].properties[i].name;
		if (idx & FLAG_PATH_PROPERTY_IS_NODE) {
			ret.push_back(names[idx & FLAG_PROP_NAME_MASK]);
		}
	}
	return ret;
}
Variant SceneState::get_node_property_value(int p_idx, int p_prop) const {
	ERR_FAIL_INDEX_V(p_idx, nodes.size(), Variant());
	ERR_FAIL_INDEX_V(p_prop, nodes[p_idx].properties.size(), Variant());
	return variants[nodes[p_idx].properties[p_prop].value];
}
NodePath SceneState::get_node_owner_path(int p_idx) const {