Пример кода<?
require($_SERVER['DOCUMENT_ROOT'] . '/bitrix/modules/main/include/prolog_before.php');
CModule::IncludeModule('iblock');
$iblockId = 14; // ID вашего инфоблока
$propertyList = CIBlockProperty::GetList([], ['IBLOCK_ID' => $iblockId]);
while ($property = $propertyList->Fetch()) {
    CIBlockProperty::Update($property['ID'], [
        'IBLOCK_ID' => $iblockId,
        'SMART_FILTER' => 'Y'
    ]);
}
?>