Entity references set with Inline Entity Form disappear when clicking to Seo preview button and saving the node

I can confirm that this module breaks the entity reference fields (in my case with Media Library widget) where the weight of the items is not saved.

The problem is most likely related with changing the handler class for entity forms in yoast_seo.module:

function yoast_seo_entity_type_build(array &$entity_types) {
  /** @var \Drupal\Core\Entity\EntityTypeInterface[] $entity_types */
  foreach ($entity_types as &$entity_type) {
    if (!$entity_type->hasHandlerClass('yoast_seo_preview_form')) {
      $entity_type->setHandlerClass('yoast_seo_preview_form', AnalysisFormHandler::class);
    }
  }
}

Commenting out the line with setHanderClass() call fixes for me the issue with item ordering.