Superseding 1040 not Processed?

Anybody successfully file a superseding 1040?

I filed my original return via e-file. Almost immediately after filing, I realized I blew it by forgetting to include some investment income while also failing to take advantage of the late IRA contributions made by my wife to lower our tax bill.

A week later I filed a superseding return (on paper and submitted well before the filing deadline), and paid the tax due based on that return, but it appears that the superseding return was not processed (sent it certified and have POD). I received my delinquent tax notice yesterday with interest accruing daily.

Am I screwed? Any advice would be very much appreciated.

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