Custom Crons Directory
From WHMCS Documentation
By default, the system stores cron-related items in the /crons/ directory. We recommend moving the crons directory to a custom private directory above your web root. This will prevent web-based access and help to protect your WHMCS installation.
Moving the Crons Directory
When you customize this location, you must move the directory and update WHMCS's configuration.
For steps to do this, see Moving the Crons Directory.
Upgrades and Patches
Applying updates or patches after customizing your crons directory location requires an additional step. You must upload any updated crons files from the default location to your custom directory.
If you do not move the files, you will see errors and issues with WHMCS's automation.