diff --git a/hed/schema/hed_schema.py b/hed/schema/hed_schema.py
index 1a2ea9419..cc8d37bff 100644
--- a/hed/schema/hed_schema.py
+++ b/hed/schema/hed_schema.py
@@ -327,6 +327,8 @@ def save_as_dataframes(self, base_filename, save_merged=False):
             - File cannot be saved for some reason.
         """
         output_dfs = Schema2DF().process_schema(self, save_merged)
+        if hasattr(self, 'extras') and self.extras:
+           output_dfs.update(self.extras)
         df_util.save_dataframes(base_filename, output_dfs)
 
     def set_schema_prefix(self, schema_namespace):
diff --git a/hed/schema/hed_schema_df_constants.py b/hed/schema/hed_schema_df_constants.py
index b6c59e45c..3e61342f2 100644
--- a/hed/schema/hed_schema_df_constants.py
+++ b/hed/schema/hed_schema_df_constants.py
@@ -23,12 +23,12 @@
 PROPERTY_KEYS = [ANNOTATION_KEY, DATA_KEY, OBJECT_KEY]
 DF_SUFFIXES = {TAG_KEY, STRUCT_KEY, VALUE_CLASS_KEY,
                UNIT_CLASS_KEY, UNIT_KEY, UNIT_MODIFIER_KEY,
-               *PROPERTY_KEYS, ATTRIBUTE_PROPERTY_KEY}
+               *PROPERTY_KEYS, ATTRIBUTE_PROPERTY_KEY, PREFIXES_KEY, EXTERNAL_ANNOTATION_KEY}
 
 
 DF_EXTRA_SUFFIXES = {PREFIXES_KEY, EXTERNAL_ANNOTATION_KEY}
-DF_SUFFIXES_OMN = {*DF_SUFFIXES, *DF_EXTRA_SUFFIXES}
-
+#DF_SUFFIXES_OMN = {*DF_SUFFIXES, *DF_EXTRA_SUFFIXES}
+DF_SUFFIXES_OMN = DF_SUFFIXES
 
 section_mapping_hed_id = {
     STRUCT_KEY: None,
diff --git a/hed/schema/schema_io/df2schema.py b/hed/schema/schema_io/df2schema.py
index db43ec6f4..68ccba546 100644
--- a/hed/schema/schema_io/df2schema.py
+++ b/hed/schema/schema_io/df2schema.py
@@ -83,6 +83,8 @@ def _parse_data(self):
                                f"{len(self.fatal_errors)} issues found when parsing schema.  See the .issues "
                                f"parameter on this exception for more details.", self.name,
                                issues=self.fatal_errors)
+        extras =  {key: self.input_data[key] for key in constants.DF_EXTRA_SUFFIXES if key in self.input_data}
+        self._schema.extras = extras
 
     def _get_prologue_epilogue(self, file_data):
         prologue, epilogue = "", ""
diff --git a/tests/schema/test_hed_schema_io_df.py b/tests/schema/test_hed_schema_io_df.py
index a0bdd96ee..2750b5fd0 100644
--- a/tests/schema/test_hed_schema_io_df.py
+++ b/tests/schema/test_hed_schema_io_df.py
@@ -51,9 +51,12 @@ def test_from_dataframes(self):
         filenames = convert_filenames_to_dict(filename)
         new_file_strings = {}
         for key, value in filenames.items():
-            with open(value, "r") as f:
-                all_lines = f.readlines()
-                new_file_strings[key] = "".join(all_lines)
+            try:
+                with open(value, "r") as f:
+                    all_lines = f.readlines()
+                    new_file_strings[key] = "".join(all_lines)
+            except FileNotFoundError as e:
+                pass
 
         reloaded_schema = from_dataframes(new_file_strings)
         self.assertEqual(schema, reloaded_schema)