After you file

I was just wondering how IRS can even tell that there are duplicate 1099-R.

It is perfectly fine for the person to have two IRA accounts with the same broker and withdraw the same amount from both. 1099-R will be identical but not duplicates because accounts are different. But account number is not part of 1099-R. 

Besides, before we send our returns brokers already sent all 1099-R to IRS and no rejects. 

Very strange...