If your original return was e-filed and accepted by the IRS, but is taking longer than the typical 21 days to process, your return may have been selected for review by the IRS. This means that the IRS will send you a letter requesting documentation for credits or other entries on your tax return. It is best to sit tight and wait to hear from them to see if they make a change to your return or need additional information.
The balance due showing on your Amendment is calculated under the assumption that you have already received your original refund. I would recommend waiting until your original return processes before you file the Amendment. You may not have to file an Amendment if the IRS ends up making the adjustment on your original return.
Please see this IRS Tax Tips Article: When an IRS letter arrives, don't panic!
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