In 2019, my wife filed separately and took the standard deduction. I also filed separately, but chose to itemize my deductions. I learned later that you can only file separately if you both use the same deduction type, and also determined that filing jointly would result in a better refund, so I amended our return. I recently received a notice in the mail, addressed to both of us, that our amended return was accepted and,"if the adjustment results in a refund, and you don't owe any other taxes or ..., you will get a refund...". In our case, the TurboTax amended return results showed a refund. I few days later I was surprised see that the IRS had sent a second letter addressed only to my wife that said, "We made the changes you requested to your 2019 form 1040 to adjust your total federal income tax withheld. As a result you owe $xxx.xx." I'm confused because I thought the amended return to file jointly essentially tosses out both of our old returns, and would have expected any additional amount that she owed to essentially subtract from what we both were to receive due to our new calculated over-payment of tax based on the change in filing status. Maybe this is entirely normal and the easiest way for them to balance their books, but I'm still confused. Thanks for any advice you can provide.
