Yes, after the Form 1099-R is entered there will be a series of follow-up questions that will need to be answered.
One of those questions asked what you did with the distribution. This is where you can select that you rolled some or all of it to an IRA or other retirement account. Then, the next screen will allow you to enter the amount that was rolled back to the same account.
Go to the Form 1099-R input section to edit the imported Form 1099-R and then go through the follow-up questions.
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