From your question, I am surmising that the "X" amount owed included the penalty due to PA. If you authorized your bank to pay the X amount on April 14, then that is the amount that will be paid as of right now without contacting your financial institution.
If the actual amount now owed is the smaller amount and for which you have an actual amount known, I suggest you contact your bank to amend the amount to be paid. It will probably entail a cancellation of the original amount and the new smaller amount put in to your payment que with the bank for April 14, 2023. I also suggest you get written confirmation from your bank that the original amount to be paid is now cancelled and the new smaller amount will be the amount paid.
If you decide to let the larger amount be paid inclusive of the underpayment penalty that was waived, the PA Department of Revenue will either refund the amount to you eventually, or credit the amount to your 2023 tax liability. You should receive a letter if the full payment goes through as to what you want to do regarding the overpayment.
PA Dept of Revenue Overpayments
@sankar_mukh
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