Rather than trying to cover the procedures for several possible scenarios, please give us some more details.
In what year did you receive the reimbursement and report it as income on your tax return?
In what year did you pay it back?
How much was the reimbursement? Was it all included in the wages in box 1 of your W-2 in the year that you received it? How much did you pay back? Please give exact amounts. One dollar could make a big difference in how you handle it.
Why did you have to pay it back?
I don't understand what you mean by the repayment being "almost 30% higher than the reimbursement due to taxes and etc." Was the repayment higher than the amount reported as income on your W-2, or do you mean that it was higher than the net amount you received, after taxes? Exact numbers might help here, too.
