sku+items+sections

$sql = [
    'select' => [
        "ID",
    ],
    'runtime' => [
        new \Bitrix\Main\Entity\ReferenceField( // получим свойство связи с SKU
            'CML2_LINK',
            '\Bitrix\Iblock\PropertyTable',
            [
                "=ref.CODE" => new \Bitrix\Main\DB\SqlExpression('?', 'CML2_LINK'),
            ],
            ["join_type" => "left"]
        ),
        new \Bitrix\Main\Entity\ReferenceField( // получим свойство артикула
            'CML2_ARTICLE',
            '\Bitrix\Iblock\PropertyTable',
            [
                "=ref.CODE" => new \Bitrix\Main\DB\SqlExpression('?', 'CML2_ARTICLE'),
            ],
            ["join_type" => "left"]
        ),
        new \Bitrix\Main\Entity\ReferenceField( // получим свойство штрихкода
            'CML2_BAR_CODE',
            '\Bitrix\Iblock\PropertyTable',
            [
                "=ref.CODE" => new \Bitrix\Main\DB\SqlExpression('?', 'CML2_BAR_CODE'),
            ],
            ["join_type" => "left"]
        ),
        new \Bitrix\Main\Entity\ReferenceField(
            'SKU_LINK_ID',
            '\Bitrix\Iblock\ElementPropertyTable',
            [
                "=this.ID" => "ref.VALUE",
                "=this.CML2_LINK.ID" => "ref.IBLOCK_PROPERTY_ID",
            ],
            ["join_type" => "inner"]
        ),
        new \Bitrix\Main\Entity\ReferenceField(
            'SKU_ITEM',
            '\Bitrix\Iblock\ElementTable',
            [
                "=this.SKU_LINK_ID.IBLOCK_ELEMENT_ID" => "ref.ID",
            ],
            ["join_type" => "left"]
        ),
        new \Bitrix\Main\Entity\ReferenceField(
            'SKU_ITEM_PROPERTY_CML2_ARTICLE',
            '\Bitrix\Iblock\ElementPropertyTable',
            [
                "=this.SKU_ITEM.ID" => "ref.IBLOCK_ELEMENT_ID",
                "=this.CML2_ARTICLE.ID" => "ref.IBLOCK_PROPERTY_ID",
            ],
            ["join_type" => "left"]
        ),
        new \Bitrix\Main\Entity\ReferenceField(
            'SKU_ITEM_PROPERTY_CML2_BAR_CODE',
            '\Bitrix\Iblock\ElementPropertyTable',
            [
                "=this.SKU_ITEM.ID" => "ref.IBLOCK_ELEMENT_ID",
                "=this.CML2_BAR_CODE.ID" => "ref.IBLOCK_PROPERTY_ID",
            ],
            ["join_type" => "left"]
        ),
        new \Bitrix\Main\Entity\ReferenceField(
      'SECTION',
      '\Bitrix\Iblock\SectionTable',
      [
         "=this.IBLOCK_SECTION_ID" => "ref.ID",
      ],
      ["join_type" => "left"]
   ),
   new \Bitrix\Main\Entity\ReferenceField(
      'TOP_SECTION',
      '\Bitrix\Iblock\SectionTable',
      [
         ">this.SECTION.LEFT_MARGIN" => "ref.LEFT_MARGIN",
         "<this.SECTION.RIGHT_MARGIN" => "ref.RIGHT_MARGIN",
         "=ref.DEPTH_LEVEL" => new \Bitrix\Main\DB\SqlExpression('?', '1'),
      ],
      ["join_type" => "left"]
   ),

    ],
    'group' => [
        'ID',
        //'SKU_ITEM.ID',
    ],
    'filter' => [
        "ACTIVE" => "Y",
        "IBLOCK_ID" => $arParams["IBLOCK_ID"], // только товары
        "!=TOP_SECTION.CODE" => $_SESSION["SKIP_INDEX_SECTION_CODE"],
    ],
    'order' => ['ID' => "ASC"],
    'cache' => ($arParams["CACHE_TYPE"] != "N" ? ["ttl" => $arParams["CACHE_TIME"], "cache_joins" => true] : null),
    'limit' => 50000
];
$iterator = \Bitrix\Iblock\ElementTable::getList($sql);
while ($filtredElementArr = $iterator->fetch()) {
    $ids[] = $filtredElementArr["ID"];
}