Rota has been submitted / payroll has been done - Holiday has not been put into Fourth !

In this situation we would advance the amount owed to the employee manually though the bank and capture in the payroll next week as advance / full payment. My question relates to the employee holiday allocation. I have added a holiday request however as the date has passed it cannot be authrosed and therfore the allocation has not reduced for these days taken / paid ? Is there a way around this ?