When applying a payment manually to an automatically generated invoice for a service, addon or domain, WHMCS will, along with any other automation, update the next due date.

If this is not occurring on your installation, you should open a ticket to discuss this with support.

WHMCS is unable to update the due date on a service when an invoice has been manually created as there is no link to the service(s) from that invoice.

If you require assistance with this, please open a ticket.