diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d3cbdfae4a2b..9e7a55a9fe16 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -5722,7 +5722,7 @@ def to_history_dataset_association(self, target_history, parent_id=None, add_to_
             sa_session.commit()
         return hda
 
-    def copy(self, parent_id=None, target_folder=None):
+    def copy(self, parent_id=None, target_folder=None, flush=True):
         sa_session = object_session(self)
         ldda = LibraryDatasetDatasetAssociation(
             name=self.name,
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 148a0df86212..5a92fd960e4b 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -3245,7 +3245,9 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
 
         assert collection.collection_type == "paired"
         forward_o, reverse_o = collection.dataset_instances
-        forward, reverse = forward_o.copy(copy_tags=forward_o.tags), reverse_o.copy(copy_tags=reverse_o.tags)
+        forward, reverse = forward_o.copy(copy_tags=forward_o.tags, flush=False), reverse_o.copy(
+            copy_tags=reverse_o.tags, flush=False
+        )
         self._add_datasets_to_history(history, [forward, reverse])
 
         out_data["forward"] = forward
@@ -3261,7 +3263,9 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
         forward_o = incoming["input_forward"]
         reverse_o = incoming["input_reverse"]
 
-        forward, reverse = forward_o.copy(copy_tags=forward_o.tags), reverse_o.copy(copy_tags=reverse_o.tags)
+        forward, reverse = forward_o.copy(copy_tags=forward_o.tags, flush=False), reverse_o.copy(
+            copy_tags=reverse_o.tags, flush=False
+        )
         new_elements = {}
         new_elements["forward"] = forward
         new_elements["reverse"] = reverse
@@ -3292,7 +3296,9 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
                     identifier = getattr(incoming_repeat["input"], "element_identifier", incoming_repeat["input"].name)
                 elif id_select == "manual":
                     identifier = incoming_repeat["id_cond"]["identifier"]
-                new_elements[identifier] = incoming_repeat["input"].copy(copy_tags=incoming_repeat["input"].tags)
+                new_elements[identifier] = incoming_repeat["input"].copy(
+                    copy_tags=incoming_repeat["input"].tags, flush=False
+                )
 
         self._add_datasets_to_history(history, new_elements.values())
         output_collections.create_collection(
@@ -3326,7 +3332,9 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
         else:
             raise Exception("Invalid tool parameters.")
         extracted = extracted_element.element_object
-        extracted_o = extracted.copy(copy_tags=extracted.tags, new_name=extracted_element.element_identifier)
+        extracted_o = extracted.copy(
+            copy_tags=extracted.tags, new_name=extracted_element.element_identifier, flush=False
+        )
         self._add_datasets_to_history(history, [extracted_o], datasets_visible=True)
 
         out_data["output"] = extracted_o
@@ -3409,7 +3417,7 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
             if getattr(value, "history_content_type", None) == "dataset":
                 copied_value = value.copy(copy_tags=value.tags, flush=False)
             else:
-                copied_value = value.copy()
+                copied_value = value.copy(flush=False)
             new_elements[key] = copied_value
 
         self._add_datasets_to_history(history, new_elements.values())
@@ -3429,7 +3437,7 @@ def _get_new_elements(self, history, elements_to_copy):
             if getattr(dce.element_object, "history_content_type", None) == "dataset":
                 copied_value = dce.element_object.copy(copy_tags=dce.element_object.tags, flush=False)
             else:
-                copied_value = dce.element_object.copy()
+                copied_value = dce.element_object.copy(flush=False)
             new_elements[element_identifier] = copied_value
         return new_elements
 
@@ -3597,7 +3605,7 @@ def add_copied_value_to_new_elements(new_label, dce_object):
             if getattr(dce_object, "history_content_type", None) == "dataset":
                 copied_value = dce_object.copy(copy_tags=dce_object.tags, flush=False)
             else:
-                copied_value = dce_object.copy()
+                copied_value = dce_object.copy(flush=False)
             new_elements[new_label] = copied_value
 
         new_labels_path = new_labels_dataset_assoc.file_name
@@ -3703,7 +3711,7 @@ def add_copied_value_to_new_elements(new_tags_dict, dce):
                     )
             else:
                 # We have a collection, and we copy the elements so that we don't manipulate the original tags
-                copied_value = dce.element_object.copy(element_destination=history)
+                copied_value = dce.element_object.copy(element_destination=history, flush=False)
                 for new_element, old_element in zip(copied_value.dataset_elements, dce.element_object.dataset_elements):
                     # TODO: This should be eliminated, but collections created by the collection builder
                     # don't set `visible` to `False` if you don't hide the original elements.
@@ -3763,7 +3771,7 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
             if getattr(dce_object, "history_content_type", None) == "dataset":
                 copied_value = dce_object.copy(copy_tags=dce_object.tags, flush=False)
             else:
-                copied_value = dce_object.copy()
+                copied_value = dce_object.copy(flush=False)
 
             if passes_filter:
                 filtered_elements[element_identifier] = copied_value