Your question doesn't make sense.
The only thing reported on your W-2 is new contributions made by payroll deduction (your money and employer match money are both reported on the W-2). This is in box 12 with a code "W". Be aware that your W-2 may have several box 12s, they might be called 12a, 12b, etc. but what counts is the dollar amount and the capital letter code. Box 12 reports several things including 401k contributions, so you might have entered a box 12 item and selected the wrong code. If your W-2 does have an item in box 12 with code W, you need to ask your employer why it's there.
Spending from the HSA is reported on a 1099-SA issued by the HSA bank. You either spent money this year or you didn't, and if you did, you need to report it. (Just so you know, you can spend money from an HSA at any time for qualified medical expenses even if you aren't allowed to make new contributions because you aren't enrolled in an eligible insurance plan.)
The only time the tax program needs to know the balance in your account is if you made excess (not allowed, not eligible) contributions, in which case the balance in your account is needed to calculate the penalty for excess contributions.
If your tax return is reporting that you made excess contributions and owe a penalty, double-check your W-2 entry. If your W-2 really does have an item in box 12 with code W, but your employer did not make HSA contributions for you, you need to contact your employer for a corrected W-2. That's all there is to it--the payroll company or employer can't pretend they don't know why your W-2 has a code W item because they created the W-2.
If your W-2 is incorrect and you can't get it corrected, you can file with a substitute W-2 form, but you should expect the IRS will send you a letter and bill you for the excess tax, so you will have to try and convince them that your W-2 is incorrect. Go back to the W-2 and edit it to remove the code W item, then check the box for "substitute W-2" on the page listing unusual circumstances.
