$flexformArray = t3lib_div::xml2array($flexformXml);
// Data manipulation here ...
$flexObj = t3lib_div::makeInstance('t3lib_flexformtools');
$xml = $flexObj->flexArray2Xml($flexformArray, true);

$flexformArray = GeneralUtility::xml2array($row['pi_flexform']);

// data manipulation like
$flexformArray['data']['additional']['lDEF']['settings.limit']['vDEF'] = 5;

// convert array back to flexformXML
$flexObj = GeneralUtility::makeInstance(FlexFormTools::class);
$flexFormXml = $flexObj->flexArray2Xml($flexformArray, true);