What you need to do is to force the excess contribution condition again.
Go through the HSA interview. When you get to the screen entitled "Let's enter your HSA contributions" (see screenshot below) and look at the second line: "Any contributions you personally made (not through your employer)"). Enter a number here like 1,000 (be sure to remember this amount).
This should force another round of "you have excess contributions", which should open the question that will allow you to change the withdrawal amount.
Note that the suggested withdrawal amounts will have changed since you added another $1,000 in excess contributions. That's OK; you are just trying to reopen that dialogue.
AT THIS POINT, you DON'T want to withdraw all the excess contribution, because the request for the ending balance should appear when you have an excess to carry over to 2017. The penalty is 6% of the lesser of the excess or of the HSA balance, which is why you are going to see your screen again.
Once you have changed the withdrawal amount to what you wanted in the first place, now go back to the screen entitled "Let's enter your HSA contributions" and remove that $1,000 personal contribution that you added. Step through the HSA interview to make sure that everything is the way you want it.
