diff --git a/lexical-graph/src/graphrag_toolkit/lexical_graph/storage/graph/graph_utils.py b/lexical-graph/src/graphrag_toolkit/lexical_graph/storage/graph/graph_utils.py
index 4f46e99f..b68abe69 100644
--- a/lexical-graph/src/graphrag_toolkit/lexical_graph/storage/graph/graph_utils.py
+++ b/lexical-graph/src/graphrag_toolkit/lexical_graph/storage/graph/graph_utils.py
@@ -298,6 +298,9 @@ def metadata_filter_to_opencypher_filter(f: MetadataFilter) -> str:
         else:
             raise ValueError(f'Invalid metadata filter type: {type(metadata_filter)}')
         
+    if not filter_strs:
+        return ''
+
     if metadata_filters.condition == FilterCondition.NOT:
         return f"(NOT {' '.join(filter_strs)})"
     elif metadata_filters.condition == FilterCondition.AND or metadata_filters.condition == FilterCondition.OR:
diff --git a/lexical-graph/tests/unit/storage/graph/test_graph_utils.py b/lexical-graph/tests/unit/storage/graph/test_graph_utils.py
index e87f6f2e..e58b8aa8 100644
--- a/lexical-graph/tests/unit/storage/graph/test_graph_utils.py
+++ b/lexical-graph/tests/unit/storage/graph/test_graph_utils.py
@@ -329,3 +329,30 @@ def test_passes_through_to_recursive_parser(self):
         )
         result = filter_config_to_opencypher_filters(config)
         assert "source.category = 'tech'" in result
+
+
+    def test_empty_filters_list_returns_empty_string(self):
+        """Regression test for issue #408.
+        
+        When MetadataFilters has an empty filters list, parse_metadata_filters_recursive
+        should return '' (empty string) instead of '()' (empty parentheses).
+        
+        Without this fix, the VersionManager generates invalid Cypher:
+          WHERE () AND coalesce(...)
+        which Neptune Database rejects with MalformedQueryException.
+        """
+        filters = MetadataFilters(
+            filters=[],
+            condition=FilterCondition.AND,
+        )
+        result = parse_metadata_filters_recursive(filters)
+        assert result == ''
+
+    def test_empty_filters_list_or_condition_returns_empty_string(self):
+        """Same as above but with OR condition."""
+        filters = MetadataFilters(
+            filters=[],
+            condition=FilterCondition.OR,
+        )
+        result = parse_metadata_filters_recursive(filters)
+        assert result == ''