Under Setup > Payments > Payment Gateways (if using WHMCS 7.10 or older) or Configuration > System Settings > Payment Gateways (if using WHMCS 8.0 or newer), a button labelled "Migrate Billing Agreements" is displayed. When clicked, it will migrate billing agreements from the following gateways:
MyWorks PayPal Billing Agreements
Support for others may be added in the future.