The TurboTax program will pull from the original return not the amended one. This will also be the adjusted gross income (AGI) the IRS will be looking for next year to verify your return, unless they introduce something new between now and then.
I understand your concern, keeping a copy of your amended return for your records to pull other numbers as necessary is a very good idea. Next tax season rather than transferring your information from last year you do have the option of filling the program out manually using the information from your amended records. Just remember if the AGI is used for verification next year it will have to be the original AGI from the original tax return.
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