### 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.
int parent_node = NO_PARENT_SAVED;
	if (save_node) {
		
		node_map[p_node] = idx;
		
		if (p_parent_idx == NO_PARENT_SAVED) {
			int sidx;
			if (nodepath_map.has(p_node->get_parent())) {
				sidx = nodepath_map[p_node->get_parent()];
			} else {
				sidx = nodepath_map.size();
				nodepath_map[p_node->get_parent()] = sidx;
			}
			nd.parent = FLAG_ID_IS_PATH | sidx;
		} else {
			nd.parent = p_parent_idx;
		}
		parent_node = idx;
		nodes.push_back(nd);
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		Node *c = p_node->get_child(i);
		Error err = _parse_node(p_owner, c, parent_node, name_map, variant_map, node_map, nodepath_map);
		if (err) {
			return err;
		}
	}
	return OK;
}
Error SceneState::_parse_connections(Node *p_owner, Node *p_node, HashMap<StringName, int> &name_map, HashMap<Variant, int, VariantHasher, VariantComparator> &variant_map, HashMap<Node *, int> &node_map, HashMap<Node *, int> &nodepath_map) {