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You will have to amend the 2018 tax return that was filed.
See this TurboTax support FAQ for amending a 2018 tax return - https://ttlc.intuit.com/community/amending/help/how-do-i-amend-a-return-in-turbotax/01/27579
You still had to enter the 1099-R on the return even if it will not be taxable ... a form 8606 must be populated otherwise the IRS assumes the distribution was fully taxable. Complete an amended return to get the 8606 form to respond to the IRS notice.
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