TT clearly acknowledged payment amount after amend return has not changed and is an unusual event. The problem is it ignores the prior e-payment arrangement and instructed to pay by check again. Technically, the e-payment has not been processed at that point so I do owe IRS that money.
For some reasons, it didn't offer e-payment for the amend return(which makes sense for a $0 payment) but then, it asked to write a check and send in with voucher to "complete" the amend return (after 1040-X was e-filed).
Honestly, if I knew it would do that, I would have waited a day which doesn't make a lot of difference in terms of tax consequence. But then, I got stuck between an incomplete 1040-X and uncertainty on whether the original payment was compromised somehow by the 1040-X.
Yes, it seems IRS can autodetect differences in actual and expected payment. Once decided excess amount is paid, it will issue a notice and a refund in about 4-6 weeks.
