No, you can't remove the entry from your W-2. The fact that the contribution was made by you or on your behalf necessitates the filing of form 8889-Health Savings Accounts. The Box 12 Code W information will be on file with the IRS and they will expect this form to be in your tax return as a result.
The form is an important part of identifying your eligibility to make the contribution and ensuring that it was within the allowed limits.
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