Invalid children when working with dynamic scenes due to partial extraction

## Bevy version

0.13.1

## What you did

1. Extract entities into a dynamic scene, extracting the parents but not the children.
2. Spawn the scene back in.

https://gist.github.com/tomara-x/24c4677068254e59941d5389340d7069

## What went wrong

The newly spawned `Parent` component contains references to invalid entities.

## Additional information

Reported by @tomara-x [on Discord](https://discord.com/channels/691052431525675048/749335865876021248/1217171397466521741).

Start with the linked reproduction gist and trace the dynamic-scene extraction and scene-spawning paths it exercises. Reproduce the case where parents are extracted without children, then verify that spawning the scene does not leave Parent components containing invalid entity references.

Written by the indexing model from the issue text.