To get drupal 8 config object that is mutable (changeable) you need to use config factory to get it and set it. For example
$config_factory = \Drupal::configFactory();
$config = $config_factory->getEditable('system.maintenance');
$config->set('message', 'bananas');
$config->save(TRUE);
here we set maintenance message to "bananas" :) . This could be used for some quick debuging locally or maybe you can use this in hook_update for some bigger set of updates like example here to change some config in bulk
https://www.drupal.org/docs/8/api/update-api/updating-configuration-in-…
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To quickly delete all in particular config just run
$config_factory = \Drupal::configFactory();
$config = $config_factory->getEditable('my_config.settings')->delete();