### 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.
names.write[i] = r[i];
		}
	}
	Array svariants = p_dictionary["variants"];
	if (svariants.size()) {
		int varcount = svariants.size();
		variants.resize(varcount);
		for (int i = 0; i < varcount; i++) {
			variants.write[i] = svariants[i];
		}
	} else {
		variants.clear();
	}
	nodes.resize(node_count);
	if (node_count) {
		const int *r = snodes.ptr();
		int idx = 0;
		for (int i = 0; i < node_count; i++) {
			NodeData &nd = nodes.write[i];
			nd.parent = r[idx++];
			nd.owner = r[idx++];
			nd.type = r[idx++];
			uint32_t name_index = r[idx++];
			nd.name = name_index & ((1 << NAME_INDEX_BITS) - 1);
			nd.index = (name_index >> NAME_INDEX_BITS);
			nd.index--; 
			nd.instance = r[idx++];
			nd.properties.resize(r[idx++]);
			for (int j = 0; j < nd.properties.size(); j++) {
				nd.properties.write[j].name = r[idx++];