### 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.push_back(other);
			} else {
				array.set(index, other);
			}
			dnp.base->set(base_property, array);
		} else {
			dnp.base->set(dnp.property, other);
		}
	}
	for (KeyValue<Ref<Resource>, Ref<Resource>> &E : resources_local_to_scene) {
		if (E.value->get_local_scene() == ret_nodes[0]) {
			E.value->setup_local_to_scene();
		}
	}
	
	int cc = connections.size();
	const ConnectionData *cdata = connections.ptr();
	for (int i = 0; i < cc; i++) {
		const ConnectionData &c = cdata[i];
		
		
		NODE_FROM_ID(cfrom, c.from);
		NODE_FROM_ID(cto, c.to);
		if (!cfrom || !cto) {
			continue;
		}
		Callable callable(cto, snames[c.method]);
		if (c.unbinds > 0) {
			callable = callable.unbind(c.unbinds);
		} else if (!c.binds.is_empty()) {