If the EFT file will be sent to the bank without the missing employee, then the amount on the EFT file will be the amount to confirm to the bank.
Options for paying the employee not included in the EFT file are:
1. Writing a physical check and doing nothing in Payroll
2. Voiding this employee's EFT and reprocessing either a check or another EFT for this employee.
If this missing employee needs to be included in the EFT file sent to the bank, since the payroll is logged, all the employees EFT's need to be voided and the entire payroll needs to be reprocessed. 
For either of the above solutions, voiding the check or voiding the entire payroll, since there might have been some corruption on a payroll file that caused this issue, after voiding the payroll or EFT, it is suggested to delete the time card files, and reorg your payroll (##py*) and bank (##br*) files prior to redoing the payroll.