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If IRS is already auditing your return than do not sent amended return. Wait until IRS notifies your about the results. Than you can decide if you agree with the proposed changes or if you want to challenge it. The premium tax credit is not calculated on your business return, it is on your personal return. The most common issue with the credit is that you didn't reconcile the credit on your tax return (you didn't use form 8962 with your return). I suspect, in your case the problem might be the income. You said you tripled your income in the last year? I would advice you to hire an experienced tax professional - Enrolled agent or CPA to help you with the responds to the letters and amend your return if needed.
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