### 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.
Vector<Variant> binds;
			if (c.binds.size()) {
				binds.resize(c.binds.size());
				for (int j = 0; j < c.binds.size(); j++) {
					binds.write[j] = props[c.binds[j]];
				}
			}
			const Variant **argptrs = (const Variant **)alloca(sizeof(Variant *) * binds.size());
			for (int j = 0; j < binds.size(); j++) {
				argptrs[j] = &binds[j];
			}
			callable = callable.bindp(argptrs, binds.size());
		}
		cfrom->connect(snames[c.signal], callable, CONNECT_PERSIST | c.flags | (p_edit_state == GEN_EDIT_STATE_MAIN ? 0 : CONNECT_INHERITED));
	}
	
	
	while (stray_instances.size()) {
		memdelete(stray_instances.front()->get());
		stray_instances.pop_front();
	}
	for (int i = 0; i < editable_instances.size(); i++) {
		Node *ei = ret_nodes[0]->get_node_or_null(editable_instances[i]);
		if (ei) {
			ret_nodes[0]->set_editable_instance(ei, true);
		}
	}
	return ret_nodes[0];
}
static int _nm_get_string(const String &p_string, HashMap<StringName, int> &name_map) {