### 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.
props = &variants[0];
	}
	
	const NodeData *nd = &nodes[0];
	Node **ret_nodes = (Node **)alloca(sizeof(Node *) * nc);
	bool gen_node_path_cache = p_edit_state != GEN_EDIT_STATE_DISABLED && node_path_cache.is_empty();
	HashMap<Ref<Resource>, Ref<Resource>> resources_local_to_scene;
	LocalVector<DeferredNodePathProperties> deferred_node_paths;
	for (int i = 0; i < nc; i++) {
		const NodeData &n = nd[i];
		Node *parent = nullptr;
		String old_parent_path;
		if (i > 0) {
			ERR_FAIL_COND_V_MSG(n.parent == -1, nullptr, vformat("Invalid scene: node %s does not specify its parent node.", snames[n.name]));
			NODE_FROM_ID(nparent, n.parent);
#ifdef DEBUG_ENABLED
			if (!nparent && (n.parent & FLAG_ID_IS_PATH)) {
				WARN_PRINT(String("Parent path '" + String(node_paths[n.parent & FLAG_MASK]) + "' for node '" + String(snames[n.name]) + "' has vanished when instantiating: '" + get_path() + "'.").ascii().get_data());
				old_parent_path = String(node_paths[n.parent & FLAG_MASK]).trim_prefix("./").replace("/", "@");
				nparent = ret_nodes[0];
			}
#endif
			parent = nparent;
		} else {
			
			ERR_FAIL_COND_V_MSG(n.parent != -1, nullptr, vformat("Invalid scene: root node %s cannot specify a parent node.", snames[n.name]));
			ERR_FAIL_COND_V_MSG(n.type == TYPE_INSTANTIATED && base_scene_idx < 0, nullptr, vformat("Invalid scene: root node %s in an instance, but there's no base scene.", snames[n.name]));
		}
		Node *node = nullptr;
		MissingNode *missing_node = nullptr;