No, the IRS won't adjust the amount you applied to 2024 based on your amended return. Because you applied your refund to 2024, the IRS looks at this the same as if you received the refund.
The amended return shows that you owe because the original refund was applied to your 2024 estimated taxes.
You can either pay the $2,000, or call the IRS, explain the situation, and ask them to adjust the amount applied to 2024. Follow this link for contact information.
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