### 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.
ERR_FAIL_COND(!p_dictionary.has("names"));
	ERR_FAIL_COND(!p_dictionary.has("variants"));
	ERR_FAIL_COND(!p_dictionary.has("node_count"));
	ERR_FAIL_COND(!p_dictionary.has("nodes"));
	ERR_FAIL_COND(!p_dictionary.has("conn_count"));
	ERR_FAIL_COND(!p_dictionary.has("conns"));
	
	int version = 1;
	if (p_dictionary.has("version")) {
		version = p_dictionary["version"];
	}
	ERR_FAIL_COND_MSG(version > PACKED_SCENE_VERSION, "Save format version too new.");
	const int node_count = p_dictionary["node_count"];
	const Vector<int> snodes = p_dictionary["nodes"];
	ERR_FAIL_COND(snodes.size() < node_count);
	const int conn_count = p_dictionary["conn_count"];
	const Vector<int> sconns = p_dictionary["conns"];
	ERR_FAIL_COND(sconns.size() < conn_count);
	Vector<String> snames = p_dictionary["names"];
	if (snames.size()) {
		int namecount = snames.size();
		names.resize(namecount);
		const String *r = snames.ptr();
		for (int i = 0; i < names.size(); i++) {