First, you should contact your HSA provider and ask them to refund your service fees dating back from March 2024 when your employer evidently closed your HSA without notifying you.
If your HSA custodian says that your HSA was open this whole time (all of 2024), then it's likely that your employer didn't take any money out of your HSA or close your HSA. So just pretend that your HSA was open all year. Also, it seems like the money that they added to your paychecks was a gift, since they didn't take the money out of your HSA.
then do this:
(this is the list from above, slightly edited)
1. Enter your corrected W-2 as is.
2. Go to the HSA interview (Deductions & Credits->Medical->1099-SA, MSA, HSA). Tell TurboTax that you have an HSA health account.
3. Go through the HSA interview.
4. When TurboTax asks if you took any money out of the HSA to pay expenses, answer YES.
5. Enter your 1099-SA for your medical expenses.
6. As you continue in the HSA interview, when you see the "Let's Enter [name]'s HSA contributions", enter the amount sent to your HSA (the amount with code W on your original W-2, or the sum of what showed up on your paystubs) as a PERSONAL contribution.
Enter the $1431. This is what actually got contributed, right? Ignore what your employer said.
7. Tell TurboTax that you had HDHP coverage for the whole year, and the type (Self? Family?). Yes, ignore the HMO nonsense.
8. When you get to the HSA Summary, it should show the $1,431 as a Deduction, your box 1 amount on the 1099-SA as a distribution, and otherwise zeros.
As I noted above, your employer fouled things up. If you do what I suggest, your tax numbers will be correct in that you won't have any excess contributions and pay any penalties.
However, the IRS might send you a letter some day asking about all this, so document all this.
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