### 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.
valid_source_owner = valid_source_owner->get_owner();
				}
			}
			if (!source_node || valid_source_owner == nullptr) {
				
				if (!c.callable.is_custom()) {
					valid_connections_from.push_back(c);
				}
			}
		}
		
		List<Node::GroupInfo> groups;
		p_node->get_groups(&groups);
		if (!modified_properties.is_empty() || !valid_connections_to.is_empty() || !valid_connections_from.is_empty() || !groups.is_empty()) {
			ModificationNodeEntry modification_node_entry;
			modification_node_entry.property_table = modified_properties;
			modification_node_entry.connections_to = valid_connections_to;
			modification_node_entry.connections_from = valid_connections_from;
			modification_node_entry.groups = groups;
			p_modification_table[p_root->get_path_to(p_node)] = modification_node_entry;
		}
	} else {
		AdditiveNodeEntry new_additive_node_entry;
		new_additive_node_entry.node = p_node;
		new_additive_node_entry.parent = p_root->get_path_to(p_node->get_parent());
		new_additive_node_entry.owner = p_node->get_owner();
		new_additive_node_entry.index = p_node->get_index();
		Node2D *node_2d = Object::cast_to<Node2D>(p_node);
		if (node_2d) {
			new_additive_node_entry.transform_2d = node_2d->get_relative_transform_to_parent(node_2d->get_parent());