### Godot version

4.1.beta (7b1387ff2)

### System information

Mageia 9, Linux

### Issue description

When opening an empty project in latest `master`, I get these errors:
```
ERROR: Index p_idx = -1 is out of bounds (edited_scene.size() = 1).
   at: get_scene_path (editor/scu/../editor_data.cpp:880)
ERROR: Index p_idx = -1 is out of bounds (edited_scene.size() = 1).
   at: check_and_update_scene (editor/scu/../editor_data.cpp:683)
ERROR: Index p_idx = -1 is out of bounds (edited_scene.size() = 1).
   at: set_edited_scene (editor/scu/../editor_data.cpp:745)
```

Possibly related to recent changes to restore past sessions, but there's nothing to restore in this case?

### Steps to reproduce

- Create a new project, edit it
- Quit to project manager
- Re-open the newly created project -> errors

### Minimal reproduction project

Empty project.
Ref<ConfigFile> cf;
	cf.instantiate();
	if (!DirAccess::exists(addon_path.get_base_dir())) {
		_remove_plugin_from_enabled(addon_path);
		WARN_PRINT("Addon '" + addon_path + "' failed to load. No directory found. Removing from enabled plugins.");
		return;
	}
	Error err = cf->load(addon_path);
	if (err != OK) {
		show_warning(vformat(TTR("Unable to enable addon plugin at: '%s' parsing of config failed."), addon_path));
		return;
	}
	if (!cf->has_section_key("plugin", "script")) {
		show_warning(vformat(TTR("Unable to find script field for addon plugin at: '%s'."), addon_path));
		return;
	}
	String script_path = cf->get_value("plugin", "script");
	Ref<Script> scr; 
	
	if (script_path.length() > 0) {
		script_path = addon_path.get_base_dir().path_join(script_path);
		scr = ResourceLoader::load(script_path, "Script", ResourceFormatLoader::CACHE_MODE_IGNORE);
		if (scr.is_null()) {
			show_warning(vformat(TTR("Unable to load addon script from path: '%s'."), script_path));
			return;
		}
		
		if (scr->get_instance_base_type() == StringName()) {
			if (_initializing_plugins) {