How do I exclude certain W2s from the EFT file

We have multiple companies under our corporate structure.   Employees who have worked in a sister company earlier in the year  are included in our W2 workfile build as they are now assigned to our company.  The issue is that their earnings from their previous company were reported thru ADP and we also have those same records in our work file..   How do I exclude the prior company earnings from passing to our EFT file.  There is no way that I can fild to exclude by TAX ID the W2s that were previously reported thru ADP.