diff -u b/core/modules/locale/src/LocaleConfigManager.php b/core/modules/locale/src/LocaleConfigManager.php
--- b/core/modules/locale/src/LocaleConfigManager.php
+++ b/core/modules/locale/src/LocaleConfigManager.php
@@ -122,13 +122,14 @@
   }
 
   /**
-   * Gets array of translated strings for translatable configuration.
+   * Gets array of translated strings for Locale translatable configuration.
    *
    * @param string $name
    *   Configuration object name.
    *
    * @return array
-   *   Array of translatable elements of the default configuration in $name.
+   *   Array of Locale translatable elements of the default configuration in
+   *   $name.
    */
   public function getTranslatableDefaultConfig($name) {
     if ($this->isSupported($name)) {
@@ -563,31 +564,25 @@
       foreach ($langcodes as $langcode) {
         $processed = $this->processTranslatableData($name, $active, $translatable, $langcode);
         // If the language code is not the same as the active storage
-        // language, we should update a configuration override.
+        // language, we should update the configuration override.
         if ($langcode != $active_langcode) {
           $override = $this->languageManager->getLanguageConfigOverride($langcode, $name);
-          $data = [];
-          if (!$override->isNew()) {
-            // Filter out any locale managed overrides from the existing
-            // override.
-            $data = $this->filterOverride($override->get(), $translatable);
-          }
+          // Filter out locale managed configuration keys so that translations
+          // removed from Locale will be reflected in the config override.
+          $data = $this->filterOverride($override->get(), $translatable);
           if (!empty($processed)) {
-            // Update translation data in configuration override.
+            // Merge in the Locale managed translations with existing data.
             $data = NestedArray::mergeDeepArray(array($data, $processed), TRUE);
           }
-          if (!empty($data)) {
-            // If there were translatable elements besides locale managed
-            // items, save with only those, and remove the ones managed
-            // by locale only.
-            $this->saveTranslationOverride($name, $langcode, $data);
+          if (empty($data) && !$override->isNew()) {
+            // The configuration override contains Locale overrides that no
+            // longer exist.
+            $this->deleteTranslationOverride($name, $langcode);
             $count++;
           }
-          else if (!$override->isNew()) {
-            // Delete language override if there is no data left at all.
-            // This means all prior translations in the override were locale
-            // managed.
-            $this->deleteTranslationOverride($name, $langcode);
+          elseif (!empty($data)) {
+            // Update translation data in configuration override.
+            $this->saveTranslationOverride($name, $langcode, $data);
             $count++;
           }
         }
diff -u b/core/modules/locale/src/Tests/LocaleConfigTranslationImportTest.php b/core/modules/locale/src/Tests/LocaleConfigTranslationImportTest.php
--- b/core/modules/locale/src/Tests/LocaleConfigTranslationImportTest.php
+++ b/core/modules/locale/src/Tests/LocaleConfigTranslationImportTest.php
@@ -7,6 +7,7 @@
 
 namespace Drupal\locale\Tests;
 
+use Drupal\locale\Locale;
 use Drupal\simpletest\WebTestBase;
 use Drupal\language\Entity\ConfigurableLanguage;
 use Drupal\Core\Url;
@@ -130,2 +131,95 @@
 
+  /**
+   * Test removing a string from Locale deletes configuration translations.
+   */
+  function testLocaleRemovalAndConfigOverrideDelete() {
+    // Enable locale, block and config_translation modules.
+    $this->container->get('module_installer')->install(['locale']);
+    $this->resetAll();
+
+    $admin_user = $this->drupalCreateUser(array('administer modules', 'administer site configuration', 'administer languages', 'access administration pages', 'administer permissions', 'translate interface'));
+    $this->drupalLogin($admin_user);
+
+    // Enable import of translations. By default this is disabled for automated
+    // tests.
+    $this->config('locale.settings')
+      ->set('translation.import_enabled', TRUE)
+      ->save();
+
+    // Add predefined language.
+    $this->drupalPostForm('admin/config/regional/language/add', ['predefined_langcode' => 'af'], t('Add language'));
+
+    $override = \Drupal::languageManager()->getLanguageConfigOverride('af', 'locale_test_translate.settings');
+    $this->assertEqual(['translatable_default_with_translation' => 'Locale can translate Afrikaans'], $override->get());
+
+    // Remove the string from translation to simulate a Locale removal. Note
+    // that is no current way of doing this in the UI.
+    $locale_storage = \Drupal::service('locale.storage');
+    $string = $locale_storage->findString(array('source' => 'Locale can translate'));
+    \Drupal::service('locale.storage')->delete($string);
+    // Force a rebuild of config translations.
+    $count = Locale::config()->updateConfigTranslations(['locale_test_translate.settings'], ['af']);
+    $this->assertEqual($count, 1, 'Correct count of updated translations');
+
+    $override = \Drupal::languageManager()->getLanguageConfigOverride('af', 'locale_test_translate.settings');
+    $this->assertEqual([], $override->get());
+    $this->assertTrue($override->isNew(), 'The configuration override was deleted when the Locale string was deleted.');
+  }
+
+  /**
+   * Test removing a string from Locale changes configuration translations.
+   */
+  function testLocaleRemovalAndConfigOverridePreserve() {
+    // Enable locale, block and config_translation modules.
+    $this->container->get('module_installer')->install(['locale']);
+    $this->resetAll();
+
+    $admin_user = $this->drupalCreateUser(array('administer modules', 'administer site configuration', 'administer languages', 'access administration pages', 'administer permissions', 'translate interface'));
+    $this->drupalLogin($admin_user);
+
+    // Enable import of translations. By default this is disabled for automated
+    // tests.
+    $this->config('locale.settings')
+      ->set('translation.import_enabled', TRUE)
+      ->save();
+
+    // Add predefined language.
+    $this->drupalPostForm('admin/config/regional/language/add', ['predefined_langcode' => 'af'], t('Add language'));
+
+    $override = \Drupal::languageManager()->getLanguageConfigOverride('af', 'locale_test_translate.settings');
+    // Update test configuration.
+    $override
+      ->set('translatable_no_default', 'This translation is preserved')
+      ->set('translatable_default_with_no_translation', 'This translation is preserved')
+      ->save();
+    $expected = [
+      'translatable_default_with_translation' => 'Locale can translate Afrikaans',
+      'translatable_no_default' => 'This translation is preserved',
+      'translatable_default_with_no_translation' => 'This translation is preserved'
+    ];
+    $this->assertEqual($expected, $override->get());
+
+    // Set the translated string to empty.
+    $search = array(
+      'string' => 'Locale can translate',
+      'langcode' => 'af',
+      'translation' => 'all',
+    );
+    $this->drupalPostForm('admin/config/regional/translate', $search, t('Filter'));
+    $textareas = $this->xpath('//textarea');
+    $textarea = current($textareas);
+    $lid = (string) $textarea[0]['name'];
+    $edit = array(
+      $lid => '',
+    );
+    $this->drupalPostForm('admin/config/regional/translate', $edit, t('Save translations'));
+
+    $override = \Drupal::languageManager()->getLanguageConfigOverride('af', 'locale_test_translate.settings');
+    $expected = [
+      'translatable_no_default' => 'This translation is preserved',
+      'translatable_default_with_no_translation' => 'This translation is preserved'
+    ];
+    $this->assertEqual($expected, $override->get());
+  }
+
 }