They might notice that you overpaid self employment tax and refund it, but it is doubtful. I would have mailed in the amended return with a notice explaining the issue. Wait and see if the refund you get has taken into consideration the self employment tax issue. If it hasn't then I would advise calling them and requesting guidance.
If they are no help, enter the amount you overpaid as an estimated payment on next year's return. They will notice there was no estimated payment made, and will request documentation verifying that you made it. At that time you can explain what happened.
