If you are sure that you have satisfied all RMD requirements, then in TurboTax, on the form 1099-R for your RMD withdrawal, answer that The entire distribution was an RMD then on the following page, to the question What is the RMD for your account? enter the full amount of the distribution from that IRA account. There is nothing to enter for the other IRAs.
By doing this, you are telling TurboTax that all RMDs are satisfied and TurboTax will not calculate any penalty. The information you entered in TurboTax is to enable TurboTax to calculate any penalty where applicable, and is not reported to the IRS.
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