You should not amend, you should send the IRS the information they requested in the letter. You can state you incorrectly entered the wrong amount that you paid, then included how much you paid along with proof on what you paid. Once the IRS receives the information they requested they will adjust your return & then process your return.
On your return in your account you can just correct the amount, don't amend. You can undo the amended return.How do I cancel or undo an amended return in TurboTax Online?
I had a similar situation where my tax return was audited because I had claimed my two step daughters before we were married. I was supposed to get around 7500 after the audit I only received around 3000. A few months later the irs sent me a letter saying I owed 4700 dollars because they over paid me. I spent hundreds of hours on the phone getting transferred from one person to another with absolutely no-one able to help me or even give me an explanation. The IRS has taken my last 2 tax returns and put it towards that 4700. What can I do? Please help.