### 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.
Array array = value;
					Array new_array;
					for (int i = 0; i < array.size(); i++) {
						Variant elem = array[i];
						if (elem.get_type() == Variant::OBJECT) {
							if (Node *n = Object::cast_to<Node>(elem)) {
								new_array.push_back(p_node->get_path_to(n));
								continue;
							}
						}
						new_array.push_back(elem);
					}
					value = new_array;
				}
			}
		}
		if (!pinned_props.has(name)) {
			bool is_valid_default = false;
			Variant default_value = PropertyUtils::get_property_default_value(p_node, name, &is_valid_default, &states_stack, true);
			if (is_valid_default && !PropertyUtils::is_property_value_different(value, default_value)) {
				continue;
			}
		}
		NodeData::Property prop;
		prop.name = _nm_get_string(name, name_map);
		prop.value = _vm_get_variant(value, variant_map);
		if (use_deferred_node_path_bit) {
			prop.name |= FLAG_PATH_PROPERTY_IS_NODE;
		}
		nd.properties.push_back(prop);