"Individual Contribution tax year correction. (Change INDIVIDUAL contribution from one tax reporting year to another. Please note this correction can result in a corrected 5498-SA. If multiple deposits occurred please list each deposit date and the corresponding amount.""
I have never seen an HSA custodian ask you which year you wanted it applied to. Well, it's their paperwork...
This sounds like your employer is not going to send you a corrected W-2 (since this negotiation is between you and the HSA custodian). If so, then what I said before is still true - if you file a return with numbers on your W-2 that differ from the numbers on the copy of your W-2 that the IRS has, then this will likely generate a letter from the IRS at some point. Your response would be to explain what happened.
So I would go back to your employer and ask about a corrected W-2 (I can't remember if they offered to do one or not). If yes, then file the extension, pay the amount you expect to owe (today), and file the actual return when you get the corrected W-2.
If no corrected W-2, then you can change the W-2 to correct the code W amount in box 12, but expect a letter from the IRS sooner or later.
In any case, document what happened and save it in your permanent tax file, for when you need to explain it to someone.
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