### 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.
} else if (Object::cast_to<Node2D>(ret_nodes[n.parent])) {
							obj = memnew(Node2D);
#ifndef _3D_DISABLED
						} else if (Object::cast_to<Node3D>(ret_nodes[n.parent])) {
							obj = memnew(Node3D);
#endif 
						}
					}
					if (!obj) {
						obj = memnew(Node);
					}
					node = Object::cast_to<Node>(obj);
				}
			}
		}
		if (node) {
			
			
			
			int nprop_count = n.properties.size();
			if (nprop_count) {
				const NodeData::Property *nprops = &n.properties[0];
				Dictionary missing_resource_properties;
				for (int j = 0; j < nprop_count; j++) {
					bool valid;
					ERR_FAIL_INDEX_V(nprops[j].value, prop_count, nullptr);
					if (nprops[j].name & FLAG_PATH_PROPERTY_IS_NODE) {
						uint32_t name_idx = nprops[j].name & (FLAG_PATH_PROPERTY_IS_NODE - 1);
						ERR_FAIL_UNSIGNED_INDEX_V(name_idx, (uint32_t)sname_count, nullptr);
						const StringName &prop_name = snames[name_idx];