The tax code treats all payroll contributions as "employer" contributions. Basically, you agree to a salary reduction and the employer contributes the difference for you. ("Cafeteria plan" is a tax term for this type of employee benefit plan.)
For 2024 you would start the amending process, remove the deduction (which duplicated your payroll contributions). You will owe some tax. You can print and file the amended return by mail, but Turbotax may allow you to e-file a 2024 amended return (I'm not sure about this). The IRS may assess interest back dated to the original due date of 4/15/25. If the IRS assesses a penalty, you can ask for a waiver for cause, or if you never owed a penalty before, you can ask for a first-time waiver. (The penalty can be waived administratively but the interest can't be waived.)
For 2025, you can amend your return and e-file it. You could possibly amend before your payment is taken, but it would be cleaner and safer to amend after the payment is taken. You can definitely e-file an amended 2025 return. If you file the amended return and pay the difference before 4/15/25, there will be no interest or late fees. If you are more than 1 day late but less than 1 month late, any interest and penalties would be less than 1% of the balance owed.
