### 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.
ERR_FAIL_COND(!instantiated_node);
				bool original_node_is_displayed_folded = original_node->is_displayed_folded();
				bool original_node_scene_instance_load_placeholder = original_node->get_scene_instance_load_placeholder();
				
				instantiated_node->set_name(original_node->get_name());
				
				String original_node_file_path = original_node->get_scene_file_path();
				if (current_edited_scene == original_node) {
					instantiated_node->set_scene_instance_state(original_node->get_scene_instance_state());
					
					if (original_node_file_path.is_empty()) {
						Ref<SceneState> state = current_packed_scene->get_state();
						state->set_path(current_packed_scene->get_path());
						instantiated_node->set_scene_inherited_state(state);
						instantiated_node->set_scene_file_path(String());
					}
					editor_data.set_edited_scene_root(instantiated_node);
					current_edited_scene = instantiated_node;
					if (original_node->is_inside_tree()) {
						SceneTreeDock::get_singleton()->set_edited_scene(current_edited_scene);
						original_node->get_tree()->set_edited_scene_root(instantiated_node);
					}
				}
				
				original_node->replace_by(instantiated_node, false);
				
				original_node->queue_free();
				
				instantiated_node->set_display_folded(original_node_is_displayed_folded);
				instantiated_node->set_scene_instance_load_placeholder(original_node_scene_instance_load_placeholder);