Paypal IPN is their to match all paypal transactions etc. between the paypal interface and your WHMCS
Instant Payment Notification (IPN) is a message service that notifies you of events related to PayPal transactions. You can use it to automate back-office and administrative functions, such as fulfilling orders, tracking customers, and providing status and other information related to a transaction.
also to use the Paypal gateway within WHMCS is states (You must enable IPN inside your PayPal account and set the URL to)