Make notes of the net checks distributed. Create a duplicate check number for each and post each to Employee Advance. Add it as a payroll item if you do not have already.
Void issued payroll checks. Install update. Run payroll again for correct taxing. Go into each check detail before saving and enter deduction from net to the employee advance item. Each new payroll check will be zero but taxes will be correct. Next period when you run payroll you will deduct remaining advance amounts from each employee.