### 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.
}
			}
			
			if (p_edit_state == GEN_EDIT_STATE_MAIN) {
				_sanitize_node_pinned_properties(node);
			} else {
				node->remove_meta("_edit_pinned_properties_");
			}
		}
		if (missing_node) {
			missing_node->set_recording_properties(false);
		}
		ret_nodes[i] = node;
		if (node && gen_node_path_cache && ret_nodes[0]) {
			NodePath n2 = ret_nodes[0]->get_path_to(node);
			node_path_cache[n2] = i;
		}
	}
	for (const DeferredNodePathProperties &dnp : deferred_node_paths) {
		
		Node *other = dnp.base->get_node_or_null(dnp.path);
		const String string_property = dnp.property;
		if (string_property.contains("/indices/")) {
			
			const String base_property = string_property.get_slice("/", 0);
			const int index = string_property.get_slice("/", 2).to_int();
			bool valid;
			Array array = dnp.base->get(base_property, &valid);
			ERR_CONTINUE(!valid);
			if (array.size() >= index) {