Keep the notice you received for your records. As long as there was nothing wrong with the actual numbers on your Form W2 (i.e. your wages were wrong and you received an actual corrected W2), then you do not need to amend to change the EIN. Your return will show the same calculations, so there would be nothing to process in the amendment. Also, your total reported wages will equal the amount that the IRS will have on file for you as well as your withholding amounts. But, you should keep the notice in your records and be prepared to send a copy of it if the IRS were to ever want clarification on the discrepancy. If they did, you could just send a copy of the notice showing the correct EIN.
