The Section 1341 deduction or credit is specifically for repayment of an amount that you reported as income in an earlier year. When the repayment is in the same year that you received the income, the employer should adjust your W-2. Since there's still time before the end of the year, making the adjustment should not be a big deal for them. I don't know how strong the legal obligation is for them to make the adjustment, and I can't cite a authoritative source.
Have you spoken to anyone in the Payroll department? HR might not be aware of what Payroll is doing. And don't rely on HR for tax advice.
I don't know what the solution is if the employer refuses to adjust the W-2.
