I had paid one amount through bank for one purchase invoice last month . now its missing in bank statement even its showing full paid in purchase invoice.
Have a look at the transaction which is making purchase invoice as paid. Maybe the transaction is crediting different bank account.
When you go to Purchase Invoices tab, there is a Balance due column which is clickable and will show you transactions related to each purchase invoice. This way you can find specific transaction which has market the invoice as paid.