Magento Update Up-Sells

    foreach($collection as $p) {
        $upsell = $p->getUpSellProductIds();

        if ( count($upsell) > 0 ) {
            $toUpdate = false;

            foreach ($upsell as $k => $u) {

                // Check if the entity_id is among the discontinued products
                if ( isset($discontinued[ $u ]) ) {
                    // Remove the discontinued entity from the up-sells list
                    unset($upsell[$k]);
                    $toUpdate = true;
                }
            }

            if ($toUpdate) {
                $upsellToSave = array();

                foreach ($upsell as $u) // Formatting the data
                    $upsellToSave[ $u ] = array('position'=>'');

                try {
                    $p->setUpSellLinkData($upsellToSave)->save();
                } catch (Exception $e) {
                    echo "Problem saving up-sell data.\n";
                }
            }
        }
    }

// http://magento.stackexchange.com/posts/130802