### 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_V(p_idx, nodes.size(), NodePath());
	if (nodes[p_idx].parent < 0 || nodes[p_idx].parent == NO_PARENT_SAVED) {
		if (p_for_parent) {
			return NodePath();
		} else {
			return NodePath(".");
		}
	}
	Vector<StringName> sub_path;
	NodePath base_path;
	int nidx = p_idx;
	while (true) {
		if (nodes[nidx].parent == NO_PARENT_SAVED || nodes[nidx].parent < 0) {
			sub_path.insert(0, ".");
			break;
		}
		if (!p_for_parent || p_idx != nidx) {
			sub_path.insert(0, names[nodes[nidx].name]);
		}
		if (nodes[nidx].parent & FLAG_ID_IS_PATH) {
			base_path = node_paths[nodes[nidx].parent & FLAG_MASK];
			break;
		} else {
			nidx = nodes[nidx].parent & FLAG_MASK;
		}
	}
	for (int i = base_path.get_name_count() - 1; i >= 0; i--) {
		sub_path.insert(0, base_path.get_name(i));
	}
	if (sub_path.is_empty()) {