Do you get the problem on all your credit notes or just one customer? You may want to try the Recalculate Customer Balance option to recalculate the balances. To do that, please click on View menu > Customers > select (highlight) the customer from the Customer window > go the Customer menu > Recalculate Customer Balance > confirm you want to Recalculate.
In regard to your other question. When you sync both programs, it will only update Inventoria's inventory levels from other programs when you create invoices. Changes need to be done in Inventoria, when you change something in Express Invoice, it will not be reflected in Inventoria.