If your company received a deduction for the HSA contribution on your 1120-S then you can't get a deduction for the same amount on your personal return.
So you would enter the amount contributed on your behalf directly into the deductions and credits section as a contribution made on your behalf by your employer.
Go to the deductions and credits section and scroll down to medical. Answer all of the questions about your HSA until you reach the section asking if your employer made any contributions to your HSA not reported in box 12 of your W2. Answer yes to that and then enter the $4000 into the third block (other employer contributions not reported in box 12).
The next question is whether you had a high deductible health plan and once you answer yes to that and indicate the type of coverage it will show the contribution from your S-Corp and you won't be taxed for it.
@leo820
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