In Feb. 2019 we sent an amended return to the IRS noting that in 2018 we had mistakenly funded a traditional IRA for 2017 instead of a Roth. We paid the taxes due for 2017, converted the TIRA to a Roth, and after receiving our acceptance letter from the IRS paid the penalty. Now we've gotten a 1099-R from the bank (which suggested the conversion as the easiest way to fix this) noting the Roth conversion as fully taxable for 2019. We paid the taxes with our amended return. How do we fix this?
You will have to amend your 2017 tax return again to put it back the way it was originally, and report the Roth conversion on your 2019 tax return. You report transactions when they actually occur, not when you intended them to occur. You actually made a traditional IRA contribution in 2017 and you actually did a Roth conversion in 2019. That's the way you have to report it. The fact that you wish you had done it differently does not change what actually occurred.
How to I avoid paying the taxes twice? The IRS already accepted the 2017 amended return and the 2017 taxes we paid. They're not going to send the taxes back!