Foreach vypracuje akciu len raz...

...
foreach ($files as $data) {
      list($ean, $ine) = explode("|", $data);
      echo "<tr>\n";
	$stranka=file_get_contents("http://adresa.sk/".$ine);
	preg_match("~<div >(.+?)<span class=\"bigPrice\">~s", $stranka, $obsah);
	$zapis = stripslashes(substr($obsah[0], 6, -61));
	mysql_query("UPDATE test SET obsah = '$zapis' WHERE kod = '".strtoupper($ean)."' AND obsah = ''"); // AND obsah = ''
      echo "<td>".$i++.". ".strtoupper($ean)."</td><td>$ine</td>\n"; // Jednotlivý výpis e-mailov
      echo "</tr>\n";
  }

<?php
$pripoj = mysql_connect("localhost","?","?");
mysql_select_db("?", $pripoj);

   $file = "data.csv"; // Názov suboru
   $files = file($file); // Vypis zo suboru

   echo "<title>Spracovanie súboru</title>";
   echo "<table border=\"1\">\n";

   echo "<tr>\n";
   echo "<th>Kód produktu</th>\n";
   echo "<th>Typ</th>\n";
   echo "</tr>\n";
   $i = 1;
   foreach ($files as $data) {
      list($ean, $ine) = explode("|", $data);
      echo "<tr>\n";
      $stranka=file_get_contents("http://adresa.sk/".$ine);
      $obsahy = preg_match("~<div >(.+?)<span class=\"bigPrice\">~s", $stranka, $obsah);
      $zapis = stripslashes(substr($obsah[0], 6, -61));
      mysql_query("UPDATE test SET obsah = '$zapis' WHERE kod = '".strtoupper($ean)."' AND obsah = ''");
      echo "<td>".$i++.". ".strtoupper($ean)."</td><td>$ine</td>\n";
      echo "</tr>\n";
  }
      echo "</table>\n";
?>