When you try to regenerate Apache configs you may see the following error message:
Error: New files of configuration for Apache web server were not built due to errors in configuration templates. The detailed error message was e-mailed to you, so please check the e-mail, fix the errors, and click here to retry generating configuration.
Some domains with physical hosting have missed system users or vhosts directories.
Download and run Webserver Configuration Checker for detect broken domains/system users/hosting and restore subscriptions from backup if exists after removing them. If there is no backup, you can try to remove the offending subscription and recreate it again by saving content of subscription and restore it after the recreation.