### 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.
}
	
	
	List<Node::GroupInfo> groups;
	p_node->get_groups(&groups);
	for (const Node::GroupInfo &gi : groups) {
		if (!gi.persistent) {
			continue;
		}
		bool skip = false;
		for (const SceneState::PackState &ia : states_stack) {
			
			if (ia.state->is_node_in_group(ia.node, gi.name)) {
				skip = true;
				break;
			}
		}
		if (skip) {
			continue;
		}
		nd.groups.push_back(_nm_get_string(gi.name, name_map));
	}
	
	
	
	
	if (p_node == p_owner) {
		
		nd.owner = -1;
	} else if (p_node->get_owner() == p_owner) {