### 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.
ERR_FAIL_COND_V_MSG(node_path_cache.size() == 0, -1, "This operation requires the node cache to have been built.");
	if (!node_path_cache.has(p_node)) {
		if (get_base_scene_state().is_valid()) {
			int idx = get_base_scene_state()->find_node_by_path(p_node);
			if (idx != -1) {
				int rkey = _find_base_scene_node_remap_key(idx);
				if (rkey == -1) {
					rkey = nodes.size() + base_scene_node_remap.size();
					base_scene_node_remap[rkey] = idx;
				}
				return rkey;
			}
		}
		return -1;
	}
	int nid = node_path_cache[p_node];
	if (get_base_scene_state().is_valid() && !base_scene_node_remap.has(nid)) {
		
		
		
		int idx = get_base_scene_state()->find_node_by_path(p_node);
		if (idx != -1) {
			base_scene_node_remap[nid] = idx;
		}
	}
	return nid;
}
int SceneState::_find_base_scene_node_remap_key(int p_idx) const {