How to remove a deleted term entity from Entity Reference field after deleting the term entity.

remove_a_deleted_term_entity.php

<?php

use Drupal\node\NodeInterface;
use Drupal\taxonomy\TermInterface;

/**
 * Implements hook_ENTITY_TYPE_delete() for taxonomy_term entities.
 *
 * @throws \Drupal\Core\Entity\EntityStorageException
 */
function dh_extranet_taxonomy_term_delete(TermInterface $term) {
  $node_ids = _dh_extranet_load_related_nids_by_term($term);
  $nodes = Node::loadMultiple($node_ids);
  $entity_reference_class = 'Drupal\Core\Field\Plugin\Field\FieldType\EntityReferenceItem';
  foreach ($nodes as $node) {
    /** @var \Drupal\Core\Field\BaseFieldDefinition $field */
    foreach ($node->getFieldDefinitions() as $field) {
      $field_name = $field->getName();
      /** @var \Drupal\field\Entity\FieldConfig $class */
      $class = $field->getItemDefinition()->getClass();
      $is_entity_reference_class = ($class === $entity_reference_class) || is_subclass_of($class, $entity_reference_class);
      if ($is_entity_reference_class && $field->getSetting('target_type') == 'taxonomy_term') {
        _dh_extranet_remove_term_reference_from_node_field($node, $field_name, $term);
      }
    }
  }
}

/**
 * Remove term reference from a node field.
 *
 * @param \Drupal\node\NodeInterface $node
 *   The node entity.
 * @param string $field_name
 *   The field name which contains the term.
 * @param \Drupal\taxonomy\TermInterface $term
 *   The taxonomy term entity.
 *
 * @throws \Drupal\Core\Entity\EntityStorageException
 */
function _dh_extranet_remove_term_reference_from_node_field(
  NodeInterface $node,
  string $field_name,
  TermInterface $term
) {
  /** @var \Drupal\Core\Language\LanguageInterface $language */
  foreach ($node->getTranslationLanguages() as $language) {
    /** @var \Drupal\Core\Entity\ContentEntityInterface $translation */
    $translation = $node->getTranslation($language->getId());
    /** @var \Drupal\Core\Field\Plugin\Field\FieldType\EntityReferenceItem  $item */
    foreach ($translation->$field_name as $key => $item) {
      if (!$item->isEmpty() && $item->target_id == $term->id()) {
        $translation->$field_name->removeItem($key);
        $translation->save();
      }
    }
  }
}

/**
 * Load nids that are using the term in any entity reference field.
 *
 * @param \Drupal\taxonomy\TermInterface $term
 *   A taxonomy term entity.
 *
 * @return array
 *   An array with the node ids.
 */
function _dh_extranet_load_related_nids_by_term(TermInterface $term) {
  $query = Drupal::database()->select('taxonomy_index', 'ti');
  $query->fields('ti', array('nid'));
  $query->condition('ti.tid', $term->id());
  $query->distinct(TRUE);
  $node_ids = $query->execute()->fetchCol();
  if (empty($node_ids)) {
    return [];
  }

  return $node_ids;
}