After you file

I am having the exact same problem.  I have two IRAs that I took my RMDs before the change in March and decided to go on and keep the RMDs.  The Value of the IRAs is exactly the same.  In fact, I took 0% withholing on one and 15% on the other.  That way the two are different.  I submitted my tax via efile through TurboTax and the IRS rejected it becasue I submitted duplicate IRAs.  TurboTax told me to delete the duplicate which of couse I could not do because both are valid.  I reviewed the two 1099-R forms and and carefully made sure each block was correct and that the appropriate box was check to all their questions.  I resubmitted my 1040-SR again and it was just rejected.  

The only difference on the acutal 1099-R and the form for inputing the data is the box that gives the account number which has different account numbers.  Unfortunately, TurboTax does not include that box on their input form.

Has anyone figured out how to fix this issue?  I have been submitting these two IRA 1099-R forms for years without any issue.  I have been using TurboTax since 1996.