Every time I start a new project, a warning is printed about an unavailable file (due to it being referenced in `editor_layout.cfg`)

### Tested versions

v4.3.rc3.official [03afb92ef]
But I had it happening since 4.1 or so

### System information

Mac Mini M1 with newest MacOS

### Issue description

Every time I start a new project an error is printed in the console:

Again, this is when starting a completely empty project. The file Godot is looking for was indeed used in one of my old projects and it exists somewhere in some other folder and I don't see why would it be invoked. The file Godot is looking for is nothing special, it's just a special effect that is drawn on screen when the player character uses a weapon (basically a Sprite2D with maybe an audio component or something similar).

The projects work normally after I save them the first time (at least I haven't noticed anything strange) and the error message goes away after a while without me doing anything special.

This doesn't really block my work or anything but it's really annoying and slightly worrying.

### Steps to reproduce

I open a new project and get the error message. I assume it's specific to something on my end.

### Minimal reproduction project (MRP)

Godot project manager -> New project

Start in the Godot project manager by creating an empty project and observe the console warning referencing editor_layout.cfg; compare it with the old project context described in the report. Trace where that layout reference is loaded, then confirm that a new project starts without the unavailable-file warning and that the message does not recur after saving.

Written by the indexing model from the issue text.