One additional bit of information, as this appears to be a chronic problem. You have to open and save the return before selecting the update acknowledgment status. (I have no need to change anything in the return. I just re-save it.)

I just e-filed a large batch of returns and, halfway through, I noticed that many of my returns had their e-file statuses re-set to before the extensions were filed. Forms 9325 were blank until I opened the returns, saved them and then updated the e-file status. If I just tried to update, the software indicated that there were no pending e-filings that required updating.

Same thing happened last year. This is very troubling.