(You’re very welcome!) The new version of the 1040 which shows up when you do an amendment has some FYI uses, but you’re not submitting that form — just the 1040X. And there can be confusion when we read that revised 1040 like a regular one, out of the amendment context.
The 1040X (with payment) shouldn’t change the amount already applied to estimated tax, so I definitely don’t think you need to worry about somehow losing some of your money. I do like the other TurboTax expert’s idea of sending the amendment without payment (with a request to take it out of the estimated amount). I can’t find any IRS clarification that it would do this (maybe that agent has seen it though), and the worst-case-scenario is that they send you a bill with some small penalties and interest (assuming the processing doesn’t take too long).
Another idea worth a try (in my opinion) is calling the IRS first (at 800-829-1040), as discussed in this article (about seven paragraphs in). Apparently the “Internal Revenue Manual” (the not-so-behind-the-scenes procedural rules for IRS employees) mentions a undefined “hardship” scenario wherein the amount applied to estimates can be changed. With a little luck (getting a person on the line, then getting them to change it), maybe you can take care of it up front, and feel more comfortable about sending the amendment without payment.
Good luck, @jomshopper! Let us know here in the Community how this project is going, and especially what other questions are coming up...
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