TurboTax desktop version issued 1040V for new amount due with amended return, which was e-filed, but I already set up a payment when I filed the initial return. Not sure if I just wait or if I send the payment as the 1040x seems to indicate. Correction in 1040x would issue a refund.
I'm reading that you filed your original return and set up a direct debit for 4/15. Then you filed an amended return and it's for less tax than the original return, meaning you'd be due a refund? I'm not sure how the voucher comes in. When you prepare an amended tax return, you take the numbers off the original return, including the balance due or refund, and adjust them.
If you expect to owe additional money on top of what you scheduled with your original return, then you should send in the payment. If you are due a refund, meaning that the payment you scheduled was too much, and some or all of it will come back to you, I would wait for the original payment to be processed.
If this isn't the correct interpretation, please respond back here.
You can check on the status of your amended return here.