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I don't see in code part when ps_stock_available is updated. You only update quantity column in ps_product table.

query will be like this but check it first 
 

UPDATE ps_stock_available sa
LEFT JOIN ps_product p ON (sa.id_product = p.id_product)
SET sa.quantity = 'YOUR QUANTITY'
WHERE p.reference = 'YOUR-REFERENCE-CODE'

Remember to escape slash for $reference in code. You dont need to slash escape quantity value

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Anyway You should try to use build in prestashop resource like 

require_once(dirname(__FILE__).'/../../config/config.inc.php'); // path to config

// somekind of foreach or loop, while etc and put the code below into this
$product = new Product(1234); // id of product
if (Validate::isLoadedObject($product)){
    $product->quantity = 5;  // your quantity
    $product->save();
}