Hi there,
I have the same situation as the original poster of this thread. I repaid $10k to my employer. Only boxes 3 and 5 are filled out and reflecting this repayment. Box 1 is empty. If I do as you explain, then Turbotax shows to have updated everything for the amended return with a $0 refund for both fed and state. This makes no sense.
If I update box 1 with the original W2 amount - the $10k I repaid, then it shows a refund of fed tax of around 20% of the $10k amount plus a 2% amount of refund for the state tax refund. This would appear to be correct. So why is box 1 blank? I repaid $10k, so therefore I did not get those wages, so why would we put the same amount of income in Box 1, as that's what the tax is calculated off of. I'm quite confused, I'm assuming my employer (same as the poster) screwed up and did not reflect the repayment in the box 1 amount. Shouldn't they have?
