### 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_node != p_owner && p_node->get_owner() && p_node->get_owner() != p_owner && !p_owner->is_editable_instance(p_node->get_owner())) {
		return OK;
	}
	List<MethodInfo> _signals;
	p_node->get_signal_list(&_signals);
	_signals.sort();
	
	
	for (const MethodInfo &E : _signals) {
		List<Node::Connection> conns;
		p_node->get_signal_connection_list(E.name, &conns);
		conns.sort();
		for (const Node::Connection &F : conns) {
			const Node::Connection &c = F;
			if (!(c.flags & CONNECT_PERSIST)) { 
				continue;
			}
			
			
			Node *target = Object::cast_to<Node>(c.callable.get_object());
			if (!target) {
				continue;
			}
			Vector<Variant> binds;
			int unbinds = 0;
			Callable base_callable;
			if (c.callable.is_custom()) {
				CallableCustomBind *ccb = dynamic_cast<CallableCustomBind *>(c.callable.get_custom());