### Godot version

4.1 24cb43a

### System information

Windows 10 x64

### Issue description

Every time I launch Godot, I'm greeted with this in my console:
```
ERROR: Resource file not found: res://InputEventKey_7cuxk.
   at: (core\io\resource_loader.cpp:227)
```
Seems to be only happening in Project Manager and comes from this:
![](https://chat.godotengine.org/file-upload/udqZP8NQfogp4rjRL/Clipboard%20-%2021%20kwietnia%202023%2022:24)
It's part of my `editor_settings-4.tres`. I didn't test, but I think it applies to any shortcut that you customize. For some reason ResourceLoader tries to load it as a project resource, while it's a sub-resource.

Does not happen in 4.0.2.

### Steps to reproduce

1. Open Godot 4.1 project manager
2. Check the console

### Minimal reproduction project

N/A
const double time_scale = Engine::get_singleton()->get_time_scale();
	MainFrameTime advance = main_timer_sync.advance(physics_step, physics_ticks_per_second);
	double process_step = advance.process_step;
	double scaled_step = process_step * time_scale;
	Engine::get_singleton()->_process_step = process_step;
	Engine::get_singleton()->_physics_interpolation_fraction = advance.interpolation_fraction;
	uint64_t physics_process_ticks = 0;
	uint64_t process_ticks = 0;
	uint64_t navigation_process_ticks = 0;
	frame += ticks_elapsed;
	last_ticks = ticks;
	const int max_physics_steps = Engine::get_singleton()->get_max_physics_steps_per_frame();
	if (fixed_fps == -1 && advance.physics_steps > max_physics_steps) {
		process_step -= (advance.physics_steps - max_physics_steps) * physics_step;
		advance.physics_steps = max_physics_steps;
	}
	bool exit = false;
	/
	XRServer::get_singleton()->_process();
	for (int iters = 0; iters < advance.physics_steps; ++iters) {
		if (Input::get_singleton()->is_using_input_buffering() && agile_input_event_flushing) {
			Input::get_singleton()->flush_buffered_events();
		}
		Engine::get_singleton()->_in_physics = true;
		uint64_t physics_begin = OS::get_singleton()->get_ticks_usec();
		PhysicsServer3D::get_singleton()->sync();
		PhysicsServer3D::get_singleton()->flush_queries();
		PhysicsServer2D::get_singleton()->sync();
		PhysicsServer2D::get_singleton()->flush_queries();
		if (OS::get_singleton()->get_main_loop()->physics_process(physics_step * time_scale)) {