Amending a return after IRS reject

[lakedesire]

I filed my 2018 returns, and got a notice back from the IRS pertaining to missing forms.  Not sure why this happened because I had filed electronically with Turbo Tax.  I thought i had sent all the forms in response, but apparently they were still missing Schedule A.  As a result, they calculated my taxes based on the standard deduction.  I paid off the penalty letter to avoid any further interest or penalties.  Since then I received an amended document from my investment accounts, and the total of the overpayment from the standard deduction and the investment account change is over $700 per the amended return I've prepared.  But I don't know how to file this.  I started a new return as an amended return, but the 1040 that is printing does not indicate this.

[Critter]

If you did not start the amended return using the amendment process then you will not have a form 1040X in the file ... you must start over again or prepare the form by hand.  All amended returns must be mailed in ... make sure to sign it and use some sort of tracking. 

https://ttlc.intuit.com/community/amending/help/how-do-i-amend-my-return-in-the-turbotax-cd-download...