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Rebuild taxonomy_index table for all nodes
<?php
$query = \Drupal::entityQuery('node');
$ids = $query->accessCheck(FALSE)->execute();
$storage_handler = \Drupal::entityTypeManager()->getStorage('node');
// If you have a lot of nodes, you may have to split this up via
// array_chunk() instead of trying to load all nodes at one time.
$entities = $storage_handler->loadMultiple($ids);
foreach ($entities as $entity) { 
taxonomy_build_node_index($entity); 
}
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