Retirement tax questions

If you did the amendment properly by entering the Traditional IRA contribution in the IRA contribution section and specifying that is was non-deductible (TurboTax should have done that automatically if you has first entered all of your income and W-2's with the 401(k) information - TurboTax would tell you that you did not qualify for a deduction and make it non-deductible) then TurboTax would have included a 8606 form with the amended return that shows and tracks your non-deductible basis in the IRA.   That 8606 is necessary when you eventually take a distribution from the IRA.  You can never only remove the non-deductible part because it must be pro-rated over the distribution and total value of all Traditional IRA accounts.   Those calculations are done on a new 8606 form using the information from the last filed 8606 form to get the information.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**