We are NY residents but the W2 was for work in PA.
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What should probably happen is that you receive a W-2 for 2018 showing no wages in box 1, with federal tax withholding in box 2, and state tax withholding in box 17 if your state has taxes. Enter this in Turbotax just as a regular W-2, and the withheld taxes will be credited to your other taxes and will come back to you as part of your refund, assuming your total payments and withholding are more than you owe.
(You may still have Box 3 and 5 social security and medicare wages, and box 4 and 6 social security and medicare tax withheld. Because of how these taxes are collected and paid by the employer, it is a real paperwork nightmare to get them back. If your employer zeroes them out, you are lucky. If not, you can't get them back on your tax return, but they will go to your credit in the social security system which helps you earn credits towards disability and retirement income.)
I don't think you can e-file if you have a W-2 where box 2 is more than box 1, so you may have to print your return and mail it in.
If your W-2 shows the wages paid to you and is not adjusted for the repayment, contact the employer to get it corrected. If they refuse, you can adjust this in Turbotax but the IRS will probably send you a letter asking for an explanation, so make sure you keep good records for at least 6 years. A CPA might also be able to help in this case if you are using the Live Online version.
The interest you paid back is not deductible, you just eat that. (But you had the use of the money for a year, so it could have earned interest for you or done other useful things for you.)
Then for the 2017 wages repaid in 2018, there are two procedures. (Note that neither one of them will bring back your social security and medicare tax either, but it goes toward your credit at social security.)
Since the amount is over $3000, there are two ways to deal with it. The easy way is to take a special itemized deduction, it's on the Deductions and Credits page under Uncommon Deductions. But, if you don't already itemize, you won't get the full deduction, because of the way itemized deductions work.
The more complicated way is to claim an IRC 1341 Claim of Right credit. This is a direct tax credit in the amount that your 2017 taxes would have been reduced if this money hadn't been in your income. Because the tax rates were higher last year, the claim of right will save you more money than the itemized deduction even if you already itemize. But, to use the claim of right, you must have had a reasonable belief at the time that you had an unrestricted right to the money.
There are instructions in IRS publication 525 on how to calculate the amount of the credit.
https://www.irs.gov/pub/irs-pdf/p525.pdf
To enter the credit, you must make a manual adjustment directly on the tax form, as described in the instructions on Schedule 5, line 74. Enter the amount of the credit and write "IRC 1341" in the space next to the amount. To do this, you need to be using Turbotax Desktop installed on your own computer from a CD or download, and then click the Forms icon to make a direct entry on the form. (Note that this voids the accuracy guarantee.) Or in Turbotax Online, you need to upgrade to the Live version and have your CPA enter it for you.
The itemized deduction method will probably also lower your state taxes since most states accept Federal itemized deductions. If you use the claim of right procedure, you will have to investigate on your own, how to claim this in your state. If it requires a manual entry, you can make it in Forms mode, or talk to your live assistant in Turbotax Live Online.
I can't advise you on whether your facts and circumstances qualify for the claim of right. If you take it, you should keep notes or records (right down your story, with dates and other proofs) in case of audit.
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