diff --git a/core/includes/update.inc b/core/includes/update.inc
index 41667b3..f711507 100644
--- a/core/includes/update.inc
+++ b/core/includes/update.inc
@@ -894,6 +894,7 @@ function update_variables_to_config($config_name, array $variable_map) {
   // This potentially loads an existing configuration object, in case another
   // update function migrated configuration values into $config_name already.
   $config = config($config_name);
+  $original_data = $config->get();
 
   // Extract the module namespace/owner from the configuration object name.
   $module = strtok($config_name, '.');
@@ -903,7 +904,16 @@ function update_variables_to_config($config_name, array $variable_map) {
   // file, which is required to exist.
   $file = new FileStorage($config_name);
   $file->setPath(drupal_get_path('module', $module) . '/config');
-  $data = $file->read();
+  $default_data = $file->read();
+
+  // Merge any possibly existing original data into default values.
+  // Only relevant when being called repetitively on the same config object.
+  if (!empty($original_data)) {
+    $data = drupal_array_merge_deep($default_data, $original_data);
+  }
+  else {
+    $data = $default_data;
+  }
 
   // Apply the default values.
   $config->setData($data);