### 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.
HashMap<StringName, Variant> modified_properties = get_modified_properties_for_node(p_node);
		
		List<Connection> connections_to;
		p_node->get_all_signal_connections(&connections_to);
		List<ConnectionWithNodePath> valid_connections_to;
		for (const Connection &c : connections_to) {
			Node *connection_target_node = Object::cast_to<Node>(c.callable.get_object());
			if (connection_target_node) {
				
				if (!c.callable.is_custom()) {
					ConnectionWithNodePath connection_to;
					connection_to.connection = c;
					connection_to.node_path = p_node->get_path_to(connection_target_node);
					valid_connections_to.push_back(connection_to);
				}
			}
		}
		
		List<Connection> connections_from;
		p_node->get_signals_connected_to_this(&connections_from);
		List<Connection> valid_connections_from;
		for (const Connection &c : connections_from) {
			Node *source_node = Object::cast_to<Node>(c.signal.get_object());
			Node *valid_source_owner = nullptr;
			if (source_node) {
				valid_source_owner = source_node->get_owner();
				while (valid_source_owner) {
					if (valid_source_owner == p_root) {
						break;
					}