If the cancellation email is being sent because of a cancelled payment subscription, then send a different email body.

webhook-cancelled-email.php

<?php

// Copy from below this line.

/**
 * If the cancellation email is being sent because of a cancelled payment subscription,
 * then send a different email body.
 */
function my_pmpro_email_body_cancelled_subscription( $body, $email ) {
    if ( $email->template == 'cancel' && pmpro_doing_webhook() ) {
        $body = 'Your subscription has been cancelled.';
    }

    return $body;
}
add_filter( 'pmpro_email_body', 'my_pmpro_email_body_cancelled_subscription', 10, 2 );