godot: Scene is invalid/corrupt according to the Godot editor, but works normally ingame

Godot version

4.1

System information

Ubuntu 22.04.2 LTS 22.04 - Vulkan (Forward+) - integrated Intel® HD Graphics 4400 (HSW GT2) () - Intel® Core™ i7-4600U CPU @ 2.10GHz (4 Threads)

Issue description

This is the tscn file:

[gd_scene load_steps=2 format=3 uid="uid://bgrpmpmsi1ae2"]

[ext_resource type="Script" path="res://src/UI/LevelEditor/UserLevelsMenu.gd" id="1_0uvtn"]

[node name="UserLevels" type="Control" node_paths=PackedStringArray("initial_focus")]
layout_mode = 3
anchors_preset = 15
anchor_right = 1.0
anchor_bottom = 1.0
grow_horizontal = 2
grow_vertical = 2
script = ExtResource("1_0uvtn")
initial_focus = NodePath("MainContainer/Create")

[node name="MainContainer" type="VBoxContainer" parent="."]
layout_mode = 0
anchor_left = 0.5
anchor_top = 0.5
anchor_right = 0.5
anchor_bottom = 0.5
offset_left = -40.0
offset_top = -20.0
offset_right = 40.0
offset_bottom = 20.0
grow_horizontal = 2
grow_vertical = 2

[node name="Create" type="Button" parent="MainContainer"]
unique_name_in_owner = true
layout_mode = 2
button_mask = 0
text = "#create_new"

[node name="LevelContainer" type="VBoxContainer" parent="MainContainer"]
unique_name_in_owner = true
layout_mode = 2
theme_override_constants/separation = 9

[connection signal="pressed" from="MainContainer/Create" to="." method="_on_Create_pressed"]

It results in this:

And the following error: “scene/resources/packed_scene.cpp:92 - Condition “nc == 0” is true. Returning: nullptr”

It also creates adds an empty scene in the scenes tabbar, and when I click on it, it automatically closes, throwing the following two errors:

• editor/editor_data.cpp:683 - Index p_idx = 2 is out of bounds (edited_scene.size() = 2).
• editor/editor_data.cpp:745 - Index p_idx = 2 is out of bounds (edited_scene.size() = 2).

Steps to reproduce

Unknown, only happened to one of my scenes 😦

However, I can give some details surrounding the scene. I made it at some point during 4.0’s alphas. I probably never touched it since. In my git, it says it’s been unchanged for 5 months. However, I opened it yesterday. Not doing any changes to it, just opening it. It has a simple script, which opens normally.

Minimal reproduction project

Couldn’t, this happened on my major project (far too big to post)