Set the media entities thumbnail to an uploaded thumbnail.

example.module

<?php 

/**
 * Implements hook_ENTITY_TYPE_presave().
 */
function example_media_presave(EntityInterface $entity) {
  if ($entity->bundle() == 'resource') {
    if (!$entity->get('field_thumbnail')->isEmpty()) {
      $file = $entity->field_thumbnail->entity;
      $entity->set('thumbnail', $file);
    }
    else {
      // If there is nothing in the field_thumbnail then delete the existing
      // thumbnail.
      $entity->set('thumbnail');
    }
  }
}