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After you file
The part of your refund you elected to apply to this year’s estimated taxes can’t be undone on an amendment (as Fanfare wrote earlier in this thread). An amended return is to be submitted only after the original return has been completely processed, and that processing includes the overpayment (which would normally have been sent to you, but in this case has been forwarded to another department of the IRS for the estimated tax).
In the 1040 instructions (here), the IRS tells us that you can apply the amount of any additional overpayment (if there is one, on line 21 of the 1040X) to estimated taxes. And then they tell us you can’t change that election (I wish this were written more clearly, but hey—it’s the IRS!).
@jomshopper, unfortunately this means you can’t currently get back any of that money now that your refund has dropped (and it doesn’t help until later). But I hope this was helpful. Be sure to re-post with any additional questions!
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