No, you will not receive an amended 1099-SA, because this form reports on distributions, not contributions.
You may receive an amended 5498-SA (contributions) but since the form does not have to be sent to you until May 31, the original may be corrected anyway.
So go ahead and file your 2016 return. If you told TurboTax you were withdrawing the entire excess, then it was added back to line 21 on the 1040 as Other Income.
As for your excess contribution that gets withdrawn, your HSA plan administrator will send you a new 1099-SA in early 2018 in order to tell you what the earnings were for the excess contribution while it was in the HSA. You don't know the amount until you do the withdrawal, plus a lot of it is earned in 2017, so this 1099-SA will go on your 2017 return, not 2016.
Note that this 1099-SA is in addition to the regular one that you would receive if you take distributions in 2017.
So long as you actually do the withdrawal by April 18, 2017, and you tell TurboTax that you will do so, you are set for 2016.