If your W-2 does not show the excess, you don't need to do anything about it.
My guess is that Payroll was aware that the excess was made but corrected and therefore adjusted the W-2.
You say you received a 1099-SA, what does that report?
If that reports distributions you really had made, and has no reference to the excess contribution, don't do anything except report how much of your distributions were used for qualified purchases.
In other words, if the excess contribution was correct before April 15th, it's as if it never happened.
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