If you receive a message that not all EFT files have been processed when processing the End of Pay, there could be a couple of reasons why:
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:
Select all Companies, Locations and Employees.
Select the Frequency you are processing.
Select the first EFT Institution in the list.
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.
You can then produce the EFT file for the combination, marking the pays as being generated. The file can be either uploaded to the bank or discarded and you pay the employee manually through your banking software.
Alternatively, delete the transaction, correct the bank details for the employee and re-key the pay. Then produce a second bank file to be uploaded to the bank, containing just the one employee.