### 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.
case Variant::ARRAY: {
				Array varray = obj->get(E.name);
				int len = varray.size();
				for (int i = 0; i < len; i++) {
					const Variant &v = varray.get(i);
					Ref<Resource> res = v;
					if (_find_and_save_resource(res, processed, flags)) {
						ret_changed = true;
					}
				}
			} break;
			case Variant::DICTIONARY: {
				Dictionary d = obj->get(E.name);
				List<Variant> keys;
				d.get_key_list(&keys);
				for (const Variant &F : keys) {
					Variant v = d[F];
					Ref<Resource> res = v;
					if (_find_and_save_resource(res, processed, flags)) {
						ret_changed = true;
					}
				}
			} break;
			default: {
			}
		}
	}
	return ret_changed;
}
void EditorNode::_save_edited_subresources(Node *scene, HashMap<Ref<Resource>, bool> &processed, int32_t flags) {