### 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.
int idx = tool_menu->get_item_count();
	tool_menu->add_item(p_name, TOOLS_CUSTOM);
	tool_menu->set_item_metadata(idx, p_callback);
}
void EditorNode::add_tool_submenu_item(const String &p_name, PopupMenu *p_submenu) {
	ERR_FAIL_NULL(p_submenu);
	ERR_FAIL_COND(p_submenu->get_parent() != nullptr);
	tool_menu->add_child(p_submenu);
	tool_menu->add_submenu_item(p_name, p_submenu->get_name(), TOOLS_CUSTOM);
}
void EditorNode::remove_tool_menu_item(const String &p_name) {
	for (int i = 0; i < tool_menu->get_item_count(); i++) {
		if (tool_menu->get_item_id(i) != TOOLS_CUSTOM) {
			continue;
		}
		if (tool_menu->get_item_text(i) == p_name) {
			if (tool_menu->get_item_submenu(i) != "") {
				Node *n = tool_menu->get_node(tool_menu->get_item_submenu(i));
				tool_menu->remove_child(n);
				memdelete(n);
			}
			tool_menu->remove_item(i);
			tool_menu->reset_size();
			return;
		}
	}
}
PopupMenu *EditorNode::get_export_as_menu() {