"Turbo Tax thinks these entries are duplicate."
Yes, TurboTax can overreact. You might be able to just ignore the warning about duplicate entries. If not, you would get the same taxable result by changing one of the forms to have code 7, but I don't know if that would work either. Since there is no tax withholding, the fact that you changed the code will not be apparent in your filed tax return. I don't think that TurboTax is looking at the account numbers when inferring that there are duplicates, so I doubt that removing account numbers will help.
To be clear, the forms that you enter should not be identical, but even if they are not identical, TurboTax can mistakenly think that they are. The original should show $2,000 in box 1 and $1,000 in box 2a. The form that you enter for the rollover to the traditional IRA should have $1,000 in box 1 and $0 in box 2a. The one for the rollover to the Roth IRA should have $1,000 in box 1 and $1,000 in box 2a. (I assume that there is no nonzero amount in box 5.)
