If you never would have paid the $1,000, after the tax law changed, you would have owed $100. The IRS refunded you $900 of the $1,000 you paid because after the adjustments were made her tax liability was $100 instead of $1,000. Basically, you overpaid by $900. There is no need to file anything.
When you see the change on your amended form, it is including the $1,000 already paid. It is not saying that you would have originally received a $900 refund.
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