### 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.
switch (tool_menu->get_item_id(p_idx)) {
		case TOOLS_ORPHAN_RESOURCES: {
			orphan_resources->show();
		} break;
		case TOOLS_CUSTOM: {
			if (tool_menu->get_item_submenu(p_idx) == "") {
				Callable callback = tool_menu->get_item_metadata(p_idx);
				Callable::CallError ce;
				Variant result;
				callback.callp(nullptr, 0, result, ce);
				if (ce.error != Callable::CallError::CALL_OK) {
					String err = Variant::get_callable_error_text(callback, nullptr, 0, ce);
					ERR_PRINT("Error calling function from tool menu: " + err);
				}
			} 
		} break;
	}
}
void EditorNode::_export_as_menu_option(int p_idx) {