A hook for WHMCS which marks invoices which have received payment as paid, where the WHMCS system doesn't automatically mark them paid. I found that if manually associating a transaction with an invoice number in WHMCS, the invoice is not marked as paid even when there is zero total remaining. This fixes that.

mark_zero_invoices_paid.php

<?php
if (!defined("WHMCS"))
    die("This file cannot be accessed directly");

use WHMCS\Database\Capsule;

function wb_mark_zero_invoices_paid(){
    //get all unpaid invoices
    $unpaid_invoices = Capsule::table('tblinvoices')->where('status', 'Unpaid')->get();
    foreach( $unpaid_invoices as $inv ){
        $inv_id = $inv->id;
        $total = (float) $inv->total;
        //get all payments toward this invoices
        $transactions = Capsule::table('tblaccounts')->where('invoiceid', $inv_id)->get();
        foreach( $transactions as $trans ){
            $total = $total - (float) $trans->amountin; //reduce total by paid amount
        }
        //if invoice has no more outstanding dollarydoos
        if( $total <= 0 ){
            //update invoice status to PAID
            if( Capsule::table('tblinvoices')->where('id', $inv_id)->update( array('status' => 'Paid', 'datepaid' => date('Y-m-d H:i:s')) ) ){
                logActivity('Manual match: Invoice '.$inv_id.' marked as paid due to manual transaction match.', 0);
                
                //send invoice payment confirmation email
                $postData = array(
                    'messagename' => 'Invoice Payment Confirmation',
                    'id' => $inv_id
                );
                update_account_email_for_invoices( array('source'=> 'manual_match','user'=>$inv->userid, 'invoiceid'=>$inv_id, 'status'=>'Paid') );
                localAPI('SendEmail', $postData);
                fix_auto_invoice_emails();
            }
        }
    }
}
//add_hook('AddInvoicePayment', 1, "wb_mark_zero_invoices_paid"); //this hook is the obvious one, but fires at the wrong time
add_hook('PreCronJob', 1, "wb_mark_zero_invoices_paid"); //sometimes not triggered (if no automation tasks present)
add_hook('AfterCronJob', 1, "wb_mark_zero_invoices_paid"); //always triggered on cron jobs
add_hook('AdminAreaFooterOutput', 1, "wb_mark_zero_invoices_paid"); //for when a transaction is manually matched to an invoice