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.