### 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.
ERR_FAIL_INDEX(p_node, nodes.size());
	ERR_FAIL_INDEX(p_name, names.size());
	ERR_FAIL_INDEX(p_value, variants.size());
	NodeData::Property prop;
	prop.name = p_name;
	if (p_deferred_node_path) {
		prop.name |= FLAG_PATH_PROPERTY_IS_NODE;
	}
	prop.value = p_value;
	nodes.write[p_node].properties.push_back(prop);
}
void SceneState::add_node_group(int p_node, int p_group) {
	ERR_FAIL_INDEX(p_node, nodes.size());
	ERR_FAIL_INDEX(p_group, names.size());
	nodes.write[p_node].groups.push_back(p_group);
}
void SceneState::set_base_scene(int p_idx) {
	ERR_FAIL_INDEX(p_idx, variants.size());
	base_scene_idx = p_idx;
}
void SceneState::add_connection(int p_from, int p_to, int p_signal, int p_method, int p_flags, int p_unbinds, const Vector<int> &p_binds) {