There are several reasons why you might receive a message that not all EFT files have been processed when processing the End of Pay.
Restore to before EFT was exported
If you restored your database to a point before exporting the EFT file. You will need to produce the file again. You will need to verify which EFT needs to be uploaded to your banking software and only upload the correct file.
Multiple EFT Institutions
If you have multiple EFT Institutions (Company Bank Accounts), an employee may be attached to the wrong EFT Institution and they have been missed when you produced your EFT file. To find the mismatch, use EFT Export:
Go to Payroll, Transactions, Import and Export, EFT Export.
Select all for Payroll Company and Location.
Leave From Employee and To Employee blank so that all employees are included.
Select the Pay Frequency you are processing.
For EFT Institution, select the first in the list.
Select the Period End Date you are processing.
Click Preview.
If you receive a message that there are no records. Select the next EFT Institution in the list and click Preview.
You will find the mismatch because the Preview will produce a report.
Close the Preview.
You can then either produce the EFT or correct the employee record:
To produce the file:
Check that the remaining parameters are correct.
Click EFT File to produce the file. This will mark the pays as being generated. The file can be either:
uploaded to the bank.
discarded and you pay the employee manually through your banking software.
To correct the employee record:
Delete the transaction (Payroll, Transactions, Processing, Extended Timesheet).
Correct the bank details for the employee (Payroll, Maintenance, Employees, Employees).
Re-key the pay.
Then produce a second bank file to be uploaded to the bank, containing just the one employee.