Based on your description of events, I have some concern that they have taken back money from you that was still included in your W2. If I am correct, then you were taxed on money you never received. Therefore, paying them the withholding back would literally cause you to pay tax on money you never received, twice.
Therefore, the first thing that I would do is make sure that the money was never included in your W2 (the pay for the first two weeks of December), and if it was, insist that they issue a corrected W2 and amend their 4th quarter 941 to retrieve the tax. Then you can amend your return to reflect less pay and withholding.
If they did not include it in your W2, they should still correct your W2 to reflect less withholding and amend their 941 to retrieve the withholding, and you would then amend your return and pay back the IRS for any excess refund you received/tax balance you might owe.

