diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb
index 79e9aa14..f3e7b31d 100644
--- a/lib/ontologies_linked_data/models/ontology_submission.rb
+++ b/lib/ontologies_linked_data/models/ontology_submission.rb
@@ -670,8 +670,7 @@ def delete(*args)
         index_commit = options[:index_commit] == false ? false : true
 
         super(*args)
-        self.ontology.unindex(index_commit)
-        self.ontology.unindex_properties(index_commit)
+        self.ontology.unindex_all_data(index_commit)
 
         self.bring(:metrics) if self.bring?(:metrics)
         self.metrics.delete if self.metrics
diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb
index f12e1a61..d5e2eddc 100644
--- a/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb
+++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb
@@ -41,7 +41,7 @@ def index(logger, commit = true, optimize = true)
           begin
             logger.info("Indexing ontology terms: #{@submission.ontology.acronym}...")
             t0 = Time.now
-            @submission.ontology.unindex(false)
+            @submission.ontology.unindex_by_acronym(false)
             logger.info("Removed ontology terms index (#{Time.now - t0}s)"); logger.flush
 
             paging = LinkedData::Models::Class.in(@submission).include(:unmapped).aggregate(:count, :children).page(page, size)
@@ -304,4 +304,3 @@ def validate_class_ancestors(cls, logger)
     end
   end
 end
-
diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb
index d6a1b876..36dffe3e 100644
--- a/test/models/test_ontology_submission.rb
+++ b/test/models/test_ontology_submission.rb
@@ -1365,6 +1365,43 @@ def test_generate_missing_labels_sets_error_status_on_initial_page_fetch_failure
     assert_nil RequestStore.store[:requested_lang]
   end
 
+  def test_index_terms_clears_existing_term_docs_by_acronym
+    ontology = mock("ontology")
+    ontology.stubs(:bring?).with(:acronym).returns(false)
+    ontology.stubs(:bring?).with(:provisionalClasses).returns(false)
+    ontology.stubs(:acronym).returns("NPDX")
+    ontology.stubs(:provisionalClasses).returns([])
+    ontology.expects(:unindex_by_acronym).with(false)
+
+    submission = mock("submission")
+    submission.stubs(:bring?).with(:ontology).returns(false)
+    submission.stubs(:ontology).returns(ontology)
+    submission.stubs(:csv_path).returns("/tmp/npdx-classes.csv")
+    submission.stubs(:loaded_attributes).returns([:hasOntologyLanguage])
+    submission.stubs(:hasOntologyLanguage).returns(stub(skos?: true))
+
+    csv_writer = mock("csv-writer")
+    csv_writer.expects(:open).with(ontology, "/tmp/npdx-classes.csv")
+    csv_writer.expects(:close)
+    LinkedData::Utils::OntologyCSVWriter.expects(:new).returns(csv_writer)
+
+    empty_page = stub(total_pages: 0)
+    paging = mock("class-paging")
+    paging.expects(:include).with(:unmapped).returns(paging)
+    paging.expects(:aggregate).with(:count, :children).returns(paging)
+    paging.expects(:page).with(0, 2500).returns(paging)
+    paging.expects(:page).with(1, 2500).returns(paging)
+    paging.expects(:all).returns(empty_page)
+    LinkedData::Models::Class.expects(:in).with(submission).returns(paging)
+
+    indexer = LinkedData::Services::OntologySubmissionIndexer.new(submission)
+    indexer.stubs(:compute_ancestors_map).returns({})
+
+    indexer.send(:index, Logger.new(TestLogFile.new), false, false)
+  ensure
+    LinkedData::Models::Class.ancestors_cache = nil
+  end
+
   def test_skos_submission_without_skos_concept_processes_without_error
     # Regression for GH-274: SKOS submissions with no skos:Concept previously entered the
     # retry path and failed during missing-label generation because the CSV class_count