You normally do not enter data from the 5498 into TurboTax. You just put it in your tax file.
However, it sounds like you did not go through all the screens in the 1099-R interview AFTER you entered the numbers.
One question on a subsequent screen is, "what did you do with this money?" One of the options is that you rolled it over to another retirement account.
Please go back and re-run the 1099-R interview all the way through.
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