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I am in this same situation, I submitted an amended return with all the documentation stating that my withdrawal was only what I contributed to the roth. They have had they return for 5 months and keep sending me notices to pay! So stressful, was your issue resolved?
Did the documentation that you sent include the required Form 8606 Part III for reporting nonqualified Roth IRA distributions? Without that form the IRS must treat a nonqualified Roth IRA distribution as fully taxable.
I believe so, I had my CPA submit the return and I think I do remember seeing that one. The only forms I had to gather for them myself is 5498s. We called them and they said it was still in the review process but they have had the return for months! The notices are not stopping and getting more and more threatening. I almost want to go ahead and pay it until they figure it out. However, then I do not think I will ever get that money back.
I suggest contacting the Taxpayer Advocate Service within the IRS if you have not already done so: https://taxpayeradvocate.irs.gov/contact-us
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