This is my use case. We have a Drupal 8 installation that we used as decoupled, so one external API retrieve all content and them indexed. So, this external API update indexed content when Changed date is updated. But, if the content is missing it doesnt do nothing. The content is removed from index only when content is unpublished.
I was thinking in deny users to delete content, and add an state or a field value to notify that the node need to be deleted in external index. Then a while delete content with a cron.