Many older Coverdell ESA's do not track the basis, it was on your shoulders for years and you were able to send numbers when needed. There have been a lot of nonqualified errors so the program is trying to correct the issue for those not as savvy as you. You have two options:
1. You can truthfully enter the correct numbers from your records. Box 3 is how much you put in through the years towards this distribution. Box 2 is the earnings or difference between the basis and distribution.
2. The IRS instructions for Form 1099-Q, About Publication 970, Tax Benefits for Education state: "Nontaxable distributions from CESAs... are not required to be reported on your income tax return."
I understand you want to continue tracking with your return. So using your numbers may be the best option for you.
@j0mike1993
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