Simplify and fix

That last bit of the tids being assigned *outside* the if loop
(so existing, not only created ones, get used) is key.

migration_helpers.module

@@ -1,5 +1,7 @@
 <?php
 
+use Psr\Log\LogLevel;
+
 /**
  * Entity query helper.
  */
@@ -38,28 +40,69 @@ function migration_helpers_entity_query(
  * Move (and optionally filter/transform) terms between term reference fields.
  */
 function migration_helpers_move_terms(
-  $source_vocabulary,
   $destination_vocabulary,
   $source_field,
   $destination_field,
-  $source_bundle,
+  $bundle = NULL,
-  $destination_bundle = NULL,
+  $entity_type = 'node',
-  $source_entity_type = 'node',
-  $destination_entity_type = 'node',
   $mapping = [],
 ) {
-  // Destination bundle is also required but we default to making it
+
-  // the same as the source bundle.
+  /** @var \Drupal\Core\Entity\EntityTypeManagerInterface $entity_type_manager */
-  $destination_bundle ??= $source_bundle;
+  $entity_type_manager = \Drupal::service('entity_type.manager');
-    print("
+
-    $source_entity_type,
+  // Get any existing terms in destination vocabulary so we can efficiently
-    $source_bundle,
+  // prevent duplication.
-    $source_field,
+  $terms = migration_helpers_entity_query(
-    $destination_entity_type,
+    entity_type: 'taxonomy_term',
-    $destination_bundle,
+    bundle: $destination_vocabulary,
-    $destination_field,
+  );
-    $source_vocabulary,
+
-    $destination_vocabulary");
+  $term_data = [];
+  foreach ($terms as $term) {
+    $term_data[$term->id()] = $term->label();
+  }
+
+  $nodes = migration_helpers_entity_query($entity_type, $bundle, $source_field);
+  foreach ($nodes as $node) {
+    $tids = [];
+    /** @var \Drupal\node\NodeInterface $node */
+    $orig_values = $node->get($source_field);
+    foreach ($orig_values as $orig_value) {
+      $orig_tid = $orig_value->target_id;
+      $orig_term = $entity_type_manager->getStorage('taxonomy_term')->load($orig_tid);
+      $orig = $orig_term->name->value;
+      $term_name = $mapping[$orig] ?? $orig;
+      // If our map intentionally blanked out the term name, do not create
+      // a term in the new vocabulary and assign it to the destination field.
+      // Note, the term must be blanked out ('') or assigned to FALSE in the
+      // mapping, setting a term to NULL is the same as not mapping it, and it
+      // would be created in the new vocab etc.
+      if (!$term_name) {
+        continue;
+      }
+      $tid = array_search($term_name, $term_data);
+      if (empty($tid)) {
+        $new_term = $entity_type_manager->getStorage('taxonomy_term')->create([
+          'name' => $term_name,
+          'vid' => $destination_vocabulary,
+        ]);
+        $new_term->save();
+        $tid = $new_term->id();
+        \Drupal::logger('mass')->log(LogLevel::INFO, "Term $term_name created with TID $tid in vocabulary $destination_vocabulary.");
+      }
+      $tids[] = $tid;
+    }
+    // Now we have collected all the term IDs that have been created.
+    // We have to go through a surprising number of hoops to make our
+    $already_there_tids = [];
+    $already_there_values = $node->get($destination_field);
+    foreach ($already_there_values as $already_there_value) {
+      $already_there_tids[] = $already_there_value->target_id;
+    }
+    $node->set($destination_field, array_merge($tids, $already_there_tids));
+    $node->save();
+  }
 }
 
 // The below almost serve more as examples that can be followed