If you do not have a code W on the corrected W-2, and if you do not indicate that you have an HSA when you are asked about "Tell us about your Health Savings Accounts" screen, then there will be no 8889, which is fine.
As I may have told you before, please do not make entries directly on the forms, especially the 8889. It probably prevents you from e-filing, it is likely to negate your Tax Accuracy Guarantee, and it is very difficult even for tax professionals to fill in the 8889 correctly. So, no 8889, no excess contributions added to Other Income, no double taxing of your money, and finally, no problem.
You will get the money from the HSA custodian, and you will pay tax on it because of the changes to the W-2. All good.
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