diff --git a/src/azul/plugins/metadata/anvil/indexer/transform.py b/src/azul/plugins/metadata/anvil/indexer/transform.py
index a57b85a65..10eb56f1c 100644
--- a/src/azul/plugins/metadata/anvil/indexer/transform.py
+++ b/src/azul/plugins/metadata/anvil/indexer/transform.py
@@ -35,6 +35,9 @@
 from azul import (
     JSON,
 )
+from azul.collections import (
+    deep_dict_merge,
+)
 from azul.indexer import (
     BundleFQID,
     BundlePartition,
@@ -428,7 +431,31 @@ def reconcile_inner_entities(cls,
                                  ) -> tuple[JSON, BundleFQID]:
         this_entity, this_bundle = this
         that_entity, that_bundle = that
-        return that if that_bundle.version > this_bundle.version else this
+        if this_bundle.version < that_bundle.version:
+            return that
+        else:
+            if this_entity.keys() == that_entity.keys():
+                return this
+            else:
+                this_and_that = this, that
+                assert this_bundle.version == that_bundle.version, this_and_that
+                assert entity_type == 'datasets', entity_type
+
+                # FIXME: Eliminate local import
+                #        https://github.com/DataBiosphere/azul/issues/5683
+                from azul.plugins.repository.tdr_anvil import (
+                    BundleEntityType,
+                    TDRAnvilBundleFQID,
+                )
+
+                bundle_types = defaultdict(int)
+                for bundle in this_bundle, that_bundle:
+                    assert isinstance(bundle, TDRAnvilBundleFQID), this_and_that
+                    bundle_types[bundle.entity_type] += 1
+                assert bundle_types[BundleEntityType.duos] == 1, this_and_that
+                # We can safely discard that_bundle because only the version is
+                # used by the caller, and we know the versions are equal.
+                return deep_dict_merge((this_entity, that_entity)), this_bundle
 
 
 class ActivityTransformer(BaseTransformer):