Taxonomy terms disappearing
I found the issue. The taxonomy terms where stored without the taxonomy_term_hierarchy information. This info is needed for the list of terms in the admin list to determ the relations between the terms.

This was caused by me, I've removed the hierarchy field from the form. This caused Drupal to not save this information at all. There are no default values or something like that here.

https://www.drupal.org/files/drupal7-db-schema.png