I have found a bug in Magento, but I'am not sure this is bug.

app/code/core/Enterprise/Catalog/Model/Index/Action/Product/Flat/Refresh/Changelog.php

public function execute()
{
    if (!$this->_isFlatIndexerEnabled()) {
        return $this;
    }
    $this->_validate();

    $changedIds = $this->_selectChangedIds();
    if (!empty($changedIds)) {
        $stores = Mage::app()->getStores();
        foreach ($stores as $store) {
            $idsBatches = array_chunk($changedIds, Mage::helper('enterprise_index')->getBatchSize());
            foreach ($idsBatches as $ids) {
                $this->_reindex($store->getId(), $ids);
            }
        }
        $this->_setChangelogValid();
        Mage::dispatchEvent('catalog_product_flat_partial_reindex', array('product_ids' => $changedIds));
    }

    return $this;
}

So we call _reindex method for all stores by 500 products.

in _reindex method we have this code:

if (!self::$_calls) {
    $temporaryEavAttributes = $eavAttributes;

    //add status global value to the base table
    /* @var $status Mage_Eav_Model_Entity_Attribute */
    $status = $this->_productHelper->getAttribute('status');
    $temporaryEavAttributes[$status->getBackendTable()]['status'] = $status;
    //Create list of temporary tables based on available attributes attributes
    foreach ($temporaryEavAttributes as $tableName => $columns) {
        $this->_createTemporaryTable($this->_getTemporaryTableName($tableName), $columns);
    }

    //Fill "base" table which contains all available products
    $this->_fillTemporaryEntityTable($entityTableName, $entityTableColumns, $changedIds);

    //Add primary key to "base" temporary table for increase speed of joins in future
    $this->_addPrimaryKeyToTable($this->_getTemporaryTableName($entityTableName));
    unset($temporaryEavAttributes[$entityTableName]);

    foreach ($temporaryEavAttributes as $tableName => $columns) {
        $temporaryTableName = $this->_getTemporaryTableName($tableName);

        //Add primary key to temporary table for increase speed of joins in future
        $this->_addPrimaryKeyToTable($temporaryTableName);

        //Create temporary table for composite attributes
        if (isset($this->_valueTables[$temporaryTableName . $this->_valueFieldSuffix])) {
            $this->_addPrimaryKeyToTable($temporaryTableName . $this->_valueFieldSuffix);
        }

        //Fill temporary tables with attributes grouped by it type
        $this->_fillTemporaryTable($tableName, $columns, $changedIds);
    }
}

Here we create temporary table "catalog_product_entity_tmp_indexer" (and other entity type tables) if this is the first call of reindex. And we use this tmp table for update rest products (over 500)
But we have in catalog_product_entity_tmp_indexer maximum 500 products.

And partial reindex for catalog_product_flat dosn't work for changed products over 500.