You seem to be saying that TurboTax allowed the full deduction amount, but did not insert the qualified contributions note on Schedule A line 11. I don't know why it would do that. It works correctly when I try it. You might want to call TurboTax support and see if they can help. To call support go to the following link to get a phone number during the hours that support is open.
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It's not clear how you will be submitting the amended return. If you will be sending it in reply to the notice, that means you would be sending it on paper. In that case, you could just write in the note by hand on Schedule A after it is printed.
