If you go through TurboTax's "amend" process TurboTax creates a new Form 1040 with all of the correct numbers on it and all the Schedules, Forms and worksheets that support the new Form 1040. It also creates a Form 1040X which you send to the IRS, along with any Schedules and Forms that have changed from your original "as filled" income tax return.
When you start your income tax return the following year you transfer the amended income tax return, not the "as filed" income tax return. That ensures that any and all carry forwards are properly stated in the new income tax return.
