diff --git a/examples/omni/_api_client.py b/examples/omni/_api_client.py
index 75b3764b1..966f3e66c 100644
--- a/examples/omni/_api_client.py
+++ b/examples/omni/_api_client.py
@@ -160,7 +160,7 @@ def apply(
         replace: bool = False,
         write_none: bool = False,
     ) -> data_classes.ResourcesWriteResult:
-        """Add or update (upsert) items.
+        """[DEPRECATED] Add or update (upsert) items.
 
         Args:
             items: One or more instances of the pygen generated data classes.
diff --git a/examples/omni/data_classes/_cdf_external_references_listed.py b/examples/omni/data_classes/_cdf_external_references_listed.py
index e4cace0e2..6a564eb29 100644
--- a/examples/omni/data_classes/_cdf_external_references_listed.py
+++ b/examples/omni/data_classes/_cdf_external_references_listed.py
@@ -4,7 +4,14 @@
 from typing import Any, ClassVar, Literal, no_type_check, Optional, Union
 
 from cognite.client import data_modeling as dm, CogniteClient
-from cognite.client.data_classes import TimeSeries as CogniteTimeSeries
+from cognite.client.data_classes import (
+    TimeSeriesWrite as CogniteTimeSeriesWrite,
+    SequenceWrite as CogniteSequenceWrite,
+    FileMetadataWrite as CogniteFileMetadataWrite,
+    FileMetadata as CogniteFileMetadata,
+    TimeSeries as CogniteTimeSeries,
+    Sequence as CogniteSequence,
+)
 from pydantic import field_validator, model_validator
 
 from ._core import (
@@ -162,14 +169,15 @@ def as_write(self) -> CDFExternalReferencesListedWrite:
             space=self.space,
             external_id=self.external_id,
             data_record=DataRecordWrite(existing_version=self.data_record.version),
-            files=[file.as_write() if isinstance(file, FileMetadata) else file for file in self.files or []] or None,
+            files=[file.as_write() if isinstance(file, CogniteFileMetadata) else file for file in self.files or []]
+            or None,
             sequences=[
-                sequence.as_write() if isinstance(sequence, SequenceRead) else sequence
+                sequence.as_write() if isinstance(sequence, CogniteSequence) else sequence
                 for sequence in self.sequences or []
             ]
             or None,
             timeseries=[
-                timeseries.as_write() if isinstance(timeseries, TimeSeries) else timeseries
+                timeseries.as_write() if isinstance(timeseries, CogniteTimeSeries) else timeseries
                 for timeseries in self.timeseries or []
             ]
             or None,
@@ -220,12 +228,14 @@ def _to_instances_write(
         properties: dict[str, Any] = {}
 
         if self.files is not None or write_none:
-            properties["files"] = [value if isinstance(value, str) else value.external_id for value in self.files or []]
+            properties["files"] = [
+                value if isinstance(value, str) else value.external_id for value in self.files or []
+            ] or None
 
         if self.sequences is not None or write_none:
             properties["sequences"] = [
                 value if isinstance(value, str) else value.external_id for value in self.sequences or []
-            ]
+            ] or None
 
         if self.timeseries is not None or write_none:
             properties["timeseries"] = [
@@ -249,15 +259,15 @@ def _to_instances_write(
             cache.add(self.as_tuple_id())
 
         for file in self.files or []:
-            if isinstance(file, FileMetadataWrite):
+            if isinstance(file, CogniteFileMetadataWrite):
                 resources.files.append(file)
 
         for sequence in self.sequences or []:
-            if isinstance(sequence, SequenceWrite):
+            if isinstance(sequence, CogniteSequenceWrite):
                 resources.sequences.append(sequence)
 
         for timeseries in self.timeseries or []:
-            if isinstance(timeseries, TimeSeriesWrite):
+            if isinstance(timeseries, CogniteTimeSeriesWrite):
                 resources.time_series.append(timeseries)
 
         return resources
diff --git a/tests/test_integration/test_upsert.py b/tests/test_integration/test_upsert.py
index 144d5d48b..5f7fb3ab1 100644
--- a/tests/test_integration/test_upsert.py
+++ b/tests/test_integration/test_upsert.py
@@ -327,3 +327,57 @@ def test_upsert_with_cdf_external(omni_client: OmniClient, cognite_client: Cogni
             cognite_client.files.delete(id=resources.files.as_ids())
         if resources.sequences:
             cognite_client.sequences.delete(external_id=resources.sequences.as_external_ids())
+
+
+def test_upsert_with_cdf_external_listed(omni_client: OmniClient, cognite_client: CogniteClient) -> None:
+    # Arrange
+    test_name = "integration_test:upsert_with_cdf_external_listed"
+    new_item = dc.CDFExternalReferencesListedWrite(
+        external_id=f"{test_name}:Item1",
+        files=[
+            FileMetadataWrite(
+                external_id=f"{test_name}:File1",
+                name="File1",
+            )
+        ],
+        sequences=[
+            SequenceWrite(
+                external_id=f"{test_name}:Sequence1",
+                name="Sequence1",
+                columns=[
+                    SequenceColumnWrite(
+                        external_id=f"{test_name}:Column1",
+                        name="Column1",
+                        value_type="String",
+                    )
+                ],
+            )
+        ],
+        timeseries=[
+            TimeSeriesWrite(
+                external_id=f"{test_name}:TimeSeries1",
+                name="TimeSeries1",
+                metadata={"key": "value"},
+            )
+        ],
+    )
+
+    resources = dc.ResourcesWriteResult()
+    try:
+        # Act
+        resources = omni_client.upsert(new_item)
+
+        # Assert
+        assert len(resources.nodes) == 1
+        assert len(resources.time_series) == 1
+        assert len(resources.files) == 1
+        assert len(resources.sequences) == 1
+    finally:
+        if resources.nodes:
+            cognite_client.data_modeling.instances.delete(resources.nodes.as_ids())
+        if resources.time_series:
+            cognite_client.time_series.delete(external_id=resources.time_series.as_external_ids())
+        if resources.files:
+            cognite_client.files.delete(id=resources.files.as_ids())
+        if resources.sequences:
+            cognite_client.sequences.delete(external_id=resources.sequences.as_external_ids())