diff --git a/src/manage_sql.c b/src/manage_sql.c
index 93284576a..567d8ade6 100644
--- a/src/manage_sql.c
+++ b/src/manage_sql.c
@@ -58340,23 +58340,36 @@ manage_optimize (GSList *log_config, const db_conn_info_t *database,
     }
   else if (strcasecmp (name, "cleanup-config-prefs") == 0)
     {
-      int removed, fixed_values;
       sql ("DELETE FROM config_preferences WHERE id NOT IN"
            " (SELECT min(id) FROM config_preferences"
            "  GROUP BY config, type, name, value);");
-      removed = sql_changes();
 
       sql ("UPDATE config_preferences"
            " SET value = (SELECT value FROM nvt_preferences"
            "              WHERE name='scanner_plugins_timeout')"
            " WHERE name = 'scanner_plugins_timeout'"
            "   AND value = 'SCANNER_NVT_TIMEOUT';");
-      fixed_values = sql_changes();
 
-      success_text = g_strdup_printf ("Optimized: cleanup-config-prefs."
-                                      " Duplicate config preferences removed:"
-                                      " %d. Corrected preference values: %d",
-                                      removed, fixed_values);
+      sql ("UPDATE config_preferences"
+           " SET pref_nvt = NULL,"
+           "     pref_id = NULL,"
+           "     pref_type = NULL,"
+           "     pref_name = NULL"
+           " WHERE type = 'SERVER_PREFS' AND pref_nvt IS NOT NULL;");
+
+      sql ("UPDATE config_preferences"
+          " SET pref_nvt = substring (name, '^([^:]*)'),"
+          "     pref_id = CAST(substring (name, '^[^:]*:([0-9]+)') AS integer),"
+          "     pref_type = substring (name, '^[^:]*:[0-9]+:([^:]*):'),"
+          "     pref_name = substring (name, '^[^:]*:[0-9]+:[^:]*:(.*)')"
+          " WHERE type = 'PLUGINS_PREFS'"
+          "       AND (pref_nvt = '(null)' OR pref_nvt IS NULL"
+          "            OR pref_type = '(null)' OR pref_type IS NULL"
+          "            OR pref_name = '(null)' OR pref_name IS NULL)"
+          "       AND name ~ '^[^:]*:[0-9]+:[^:]*:.*'"
+          "       AND type = 'PLUGINS_PREFS';");
+
+      success_text = g_strdup_printf ("Optimized: cleanup-config-prefs.");
     }
   else if (strcasecmp (name, "cleanup-feed-permissions") == 0)
     {
diff --git a/src/manage_sql_configs.c b/src/manage_sql_configs.c
index 4fe5b0814..ae4b9454f 100644
--- a/src/manage_sql_configs.c
+++ b/src/manage_sql_configs.c
@@ -3627,6 +3627,13 @@ modify_config_preference (config_t config, const char* nvt,
           g_free (quoted_name);
           quoted_name = sql_quote (splits[3]);
         }
+      else
+        {
+          quoted_pref_nvt = sql_quote (splits[0]);
+          pref_id = atoi (splits[1]);
+          quoted_pref_type = sql_quote (splits[2]);
+          quoted_pref_name = sql_quote (splits[3]);
+        }
     }
   g_strfreev (splits);
 
@@ -3639,12 +3646,25 @@ modify_config_preference (config_t config, const char* nvt,
        config,
        nvt ? "= 'PLUGINS_PREFS'" : "= 'SERVER_PREFS'",
        quoted_name);
-  sql ("INSERT INTO config_preferences"
-       " (config, type, name, value, pref_nvt, pref_id, pref_type, pref_name)"
-       " VALUES (%llu, %s, '%s', '%s', '%s', %i, '%s', '%s');",
-       config, nvt ? "'PLUGINS_PREFS'" : "'SERVER_PREFS'", quoted_name,
-       quoted_value, quoted_pref_nvt, pref_id, quoted_pref_type,
-       quoted_pref_name);
+  if (nvt)
+    {
+      sql ("INSERT INTO config_preferences"
+          " (config, type, name, value,"
+          "  pref_nvt, pref_id, pref_type, pref_name)"
+          " VALUES (%llu, 'PLUGINS_PREFS', '%s', '%s',"
+          "         '%s', %i, '%s', '%s');",
+          config, quoted_name, quoted_value,
+          quoted_pref_nvt, pref_id, quoted_pref_type, quoted_pref_name);
+    }
+  else
+    {
+      sql ("INSERT INTO config_preferences"
+          " (config, type, name, value,"
+          "  pref_nvt, pref_id, pref_type, pref_name)"
+          " VALUES (%llu, 'SERVER_PREFS', '%s', '%s',"
+          "         NULL, NULL, NULL, NULL);",
+          config, quoted_name, quoted_value);
+    }
 
   g_free (quoted_value);
   g_free (quoted_name);