I figured it out

you have to make the changes in the original return file. not the separate copy for the amended. because the original has the "proof" that you e-filed the original. Because the data from Form 9325 doesn't flow from the original to the amended. Mine was a little more complicated. because the reason I am amending is because the client failed to give me a W-2 (he had 3). the missing W-2 was from another state where it would be an original return for that state and not an amended state.