Thanks for the tip .
$this->objectManager = \TYPO3\CMS\Core\Utility\GeneralUtility::makeInstance('TYPO3\\CMS\\Extbase\\Object\\ObjectManager');
$instObj = $this->objectManager->get('TYPO3\\CMS\\Core\\Configuration\\ConfigurationManager');
$lines = $instObj->getLocalConfigurationFileLocation();
// Get lines from Localconfiguration.php file
$localConfigurationArray = require $lines;
$instObj->removeLocalConfigurationKeysByPath( array( 'EXT/extConf/extension_key' ) ) ;
$instObj->setLocalConfigurationValueByPath( 'EXT/extConf/extension_key' , serialize($LocalconfValues) );
By this way we can overwrite values stored in Localconfiguration.php