Submitted 2016 W2 as opposed to 2017 W2 by accident

We submitted a 2016 W2 as opposed to the 2017 W2 for wages on our 2017 Tax return by accident. The return was electronically accepted by the IRS and after a month of no refund we received a letter from the IRS stating that they are in the process of conducting a thorough review. After receiving the IRS letter, we realized the error that was made (Incorrect W2). We called the Taxpayer Advocate Service (TAS) listed on the letter and they suggested submitting an Amended Return (1040X). When I go into the Turbo Tax 2017 return and attempt to perform an Amended return the refund changed dramatically from $7500 to $869 even though the W2 wage difference from 2016 and 2017 was minimal. Am I missing something here, does the IRS combine the two returns or am I doing something incorrectly within Turbo Tax.