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Unfortunately, there's a three-year deadline for filing an amended return, so you are out of luck.

I disagree. That deadline is for changing your tax for the year in question. An 8606 reporting nondeductible traditional IRA contributions has no effect on the tax for the year in question.

It seems to me that the pre-tax basis in the traditional IRA is established by the contributions, not the reporting of them on Form 8606. If OP has proof of undeducted contributions older than the 3-year limit, I'd recommending amending the open years (2003-2006), including on line 2 of the 2003 8606 all undeducted contributions for 2002 and prior.

I have no idea whether there's case law on this.

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