What I am assuming, from what you have said, is that TurboTax - when filing your original return - had added in the $300/600 charitable donation deduction to your standard deduction (after some extra work on your part).
And now that you are filing your amended return, in order to add in a 1099 that you accidentally left off of the original return, TurboTax is trying to add that same deduction to your amended return.
TurboTax is right to do that. Your amended return should be identical to the original return that you filed except for the addition of the one 1099 that you are adding. All the other deductions and income should stay on there.
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