Did you receive a CP2000 notice? You said, “The difference between what I had overpaid and the change(s) IRS made that reduced that amount available for this year's estimated payments, i.e. where they felt my filing was in error, **was exactly $400.**”
The notice adjusting your return will explain why IRS said you owed $400 more in that than you listed on your tax return. Since your tax liability went up by $400, your refund (which you applied to your estimated payment) would be reduced by $400.
You can get a free IRS transcript and compare those numbers against your original filing if you don’t have the original adjustment notice.
See Get Your Tax Record.
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