The RMD that you repaid are considered as rollovers to the same account and is not taxed.
Enter your form 1099-R normally. After entering your form 1099-R, click Continue until you reach the screen Tell us if you moved the money through a rollover or conversion. Check the radio button which corresponds to your situation then click Continue and follow the interview. Enter the amount repaid as a rollover and it will be excluded from taxation. You will still have the credit for taxes withheld.
Delete the 1099-R and re-enter.
Answer the RMD question that "None of this distribution was a RMD" or "RMD not required". The you will get the rollover question.
Sorry I do not see the screen that says "Tell us if you moved the money through a rollover or conversion. Will I find that in the IRA questions section or later?
When I look at the income summary screen it still shows that my IRA is flagged as income.
The question will come up in the Form 1099-R section where you enter the information about your distribution.