You could try calling the IRS at 800-829-1040 (it may be very difficult to get through at this time) and explaining the situation. Otherwise, I am not sure what they will do with your 1040-X, since there is really no place on it to enter a penalty, just changes to income, deductions, credits, tax, and payments. I assume you entered an explanation in Part II.
If you later receive a notice requesting payment for the underpayment penalty, you should not be charged interest on the amount shown for the penalty if you pay the amount owed in full on or before the "pay by" date on the bill.
@vasile1
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