### 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<Script> scr = Object::cast_to<Script>(p_script);
	if (scr.is_null()) {
		return;
	}
	if (p_activate_name.length()) {
		set_addon_plugin_enabled(p_activate_name, true);
	}
	project_settings_editor->update_plugins();
	project_settings_editor->hide();
	push_item(scr.operator->());
}
void EditorNode::_remove_plugin_from_enabled(const String &p_name) {