diff --git a/src/pai_rag/core/rag_configuration.py b/src/pai_rag/core/rag_configuration.py
index b9de7f49..4f916d21 100644
--- a/src/pai_rag/core/rag_configuration.py
+++ b/src/pai_rag/core/rag_configuration.py
@@ -30,12 +30,14 @@ def from_snapshot(cls):
     @classmethod
     def from_file(cls, config_file):
         try:
-            settings_files = [config_file, GENERATED_CONFIG_FILE_NAME]
+            settings_files = [config_file]
             config = Dynaconf(
                 envvar_prefix="PAIRAG",
                 settings_file=settings_files,
                 merge=True,
             )
+            snapshot_config = Dynaconf(settings_file=[GENERATED_CONFIG_FILE_NAME])
+            config.update(snapshot_config, tomlfy=True, merge=True)
             return cls(config)
             # `envvar_prefix` = export envvars with `export PAIRAG_FOO=bar`.
             # `settings_files` = Load these files in the order.
@@ -54,8 +56,6 @@ def update(self, new_value: Dynaconf):
     def persist(self):
         """Save configuration to file."""
         data = self.config.as_dict()
-        data["dynaconf_merge"] = True
-
         os.makedirs("localdata", exist_ok=True)
         loaders.write(GENERATED_CONFIG_FILE_NAME, DynaBox(data).to_dict(), merge=True)