After you enter your 1099-R you will be asked "What did you do with the money from this payer?" See the screenshot below. If you check you moved it to another retirement account, you'll see a drop down, and you can enter that you rolled all of it over.
Go through the 1099-R section again and see the screens. If you don't see it, delete your 1099-R and re-enter it, and keep going past the questions that follow until you see that screen.
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