Running sudo drush civicrm-upgrade-cfg will erase server if uploaddir is not set

Here is the chain of events.

1) CRM_Core_IDS::check calls CRM_Core_Config::singleton();
2) CRM_Core_Config::singleton(); calls _initVariables which loads the various urls & then adds a slash to them. If the url is empty it now has the value '\'
3) CRM_Core_IDS::check saves this to the IDS.php file as tmp_path ($tmpDir = empty($config->uploadDir) ? CIVICRM_TEMPLATE_COMPILEDIR : $config->uploadDir
4) The upgrade script creates a new temp folder and deletes all from the previous temp folder