### 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.
src_id = FLAG_ID_IS_PATH | nodepath_map[p_node];
				} else {
					int sidx = nodepath_map.size();
					nodepath_map[p_node] = sidx;
					src_id = FLAG_ID_IS_PATH | sidx;
				}
			}
			int target_id;
			if (node_map.has(target)) {
				target_id = node_map[target];
			} else {
				if (nodepath_map.has(target)) {
					target_id = FLAG_ID_IS_PATH | nodepath_map[target];
				} else {
					int sidx = nodepath_map.size();
					nodepath_map[target] = sidx;
					target_id = FLAG_ID_IS_PATH | sidx;
				}
			}
			ConnectionData cd;
			cd.from = src_id;
			cd.to = target_id;
			cd.method = _nm_get_string(base_callable.get_method(), name_map);
			cd.signal = _nm_get_string(c.signal.get_name(), name_map);
			cd.flags = c.flags;
			cd.unbinds = unbinds;
			for (int i = 0; i < binds.size(); i++) {
				cd.binds.push_back(_vm_get_variant(binds[i], variant_map));
			}
			connections.push_back(cd);