### 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.
const Variant &prop_variant = props[nprops[j].value];
						if (prop_variant.get_type() == Variant::ARRAY) {
							const Array &array = prop_variant;
							if (Engine::get_singleton()->is_editor_hint()) {
								if (array.get_typed_builtin() == Variant::NODE_PATH) {
									
									node->set(prop_name, prop_variant);
									continue;
								}
							}
							for (int k = 0; k < array.size(); k++) {
								DeferredNodePathProperties dnp;
								dnp.path = array[k];
								dnp.base = node;
								
								dnp.property = String(prop_name) + "/indices/" + itos(k);
								deferred_node_paths.push_back(dnp);
							}
						} else {
							
							DeferredNodePathProperties dnp;
							dnp.path = prop_variant;
							dnp.base = node;
							dnp.property = prop_name;
							deferred_node_paths.push_back(dnp);
						}
						continue;
					}
					ERR_FAIL_INDEX_V(nprops[j].name, sname_count, nullptr);
					if (snames[nprops[j].name] == CoreStringNames::get_singleton()->_script) {