<?php

$opts = $item->getProduct()->getTypeInstance(true)->getOrderOptions($item->getProduct());
$newOptions = array();
                        foreach($opts['options'] as $ops) {
                            if ($ops['label'] == "Square Ft") {
                                $ops['value'] = $actualSqFt;
                                $ops['print_value'] = $actualSqFt;
                                $ops['option_value'] = $actualSqFt;
                            }
                            $newOptions[] = $ops;
                        }
$opts['info_buyRequest']['options'][$optionId] = $actualSqFt;
$opts['options'] = $newOptions;
$item->setProductOptions($opts);
$item->save();

?>