No, if you amend, adding the 1099-R for a direct rollover will not affect your return.
Technically, since the amendment would not show any changes, you can choose to forego filing an amendment and just respond if the IRS sends you a letter about it. In that case, you would include a copy of your 1099-R and respond in writing that it was a direct rollover and therefore a non-taxable event.
If you do choose to amend, please see the following TurboTax Help Articles:
Amend TurboTax Online
Amend TurboTax CD/Download
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