Scripts removed from nodes upon loading godot, seemingly randomly

[FireCatMagic]

Godot version

4.0 stable

System information

Windows 7 64-bit

Issue description

Scripts attached to nodes seemingly randomly are no longer attached to nodes upon loading of Godot. This is found out when attempting to start the game and errors occur, and then checking out the scene where it came from.
My friend also had this same issue.

Steps to reproduce

Create a scene with a node and attatch a script
Close godot
Reopen godot
Sometimes the script is no longer attatched

Minimal reproduction project

N/A

[Calinou]

I've has this issue multiple times with the bullet.gd script in godotengine/godot-demo-projects#849, but I could never find a way to trigger this 100% of the time.

[Ezcha]

I keep having this issue as well, unsure of how to reproduce it.

[Gerporgl]

I have the same issue!

And you know what is interesting, it is only my scene called bullet.tscn with the script called bullet.gd
I've got other very similar scene with similar structure and never had that problem with those.

It is kind of annoying, since upon loading the project, if I run it I get an error, to realize the script association is gone again. I then have to re-select it in the editor (as it is empty).

For me, it seems to be doing that only on one of my 2 computers I use to edit the same project, and not always... (but it is very frequent, almost all the time I would say on that computer) that computer has a 5120 x 1440 monitor (super wide dual 1440P width), so I don't know if that could be related, I know godot always opens with the window maximized and that is also not so much desirable on that screen width... My other one has a 1920x1080 monitor.

The specs of both computers are very similar (Ryzen 3900x and 5950x CPU, AMD RX 6xxx GPUs, etc.). The OS is the same, I am on Linux Pop!_OS 22.04

[FireCatMagic]

An update - Sometimes this happens with instances. Only the root node is kept, and the script remains, but all children and the instance itself are removed.

[difof]

Same issue here, only happens with tool scripts. I cannot 100% reproduce it because it's ok on some scenes. Very strange! And I notice it when the node lose focus in scene tree. Sometimes the editor puts the script as a built-in script which is annoying because I edit code and see no changes until I figure out this happened.

[adamscott]

Same issue here, only happens with tool scripts.

Thanks for the precision. It will help debugging.

[FireCatMagic]

I do not use any tool scripts in my project and this still happens to me. My project is heavy in custom classes, though.

[Calinou]

I do not use any tool scripts in my project and this still happens to me. My project is heavy in custom classes, though.

godotengine/godot-demo-projects#849 doesn't use any @tool scripts either.

[Calinou]

Closing in favor of #76641, which has precise reproduction steps.