The amount of tax that was withheld from the bonus doesn't matter. Your bonus was $15,057.40. That amount should have been included in the wages in box 1 of your W-2 for 2017, so that's the amount of additional income you reported on your 2017 tax return.
I don't understand "taking taxes into account." When you repaid part of the bonus, you wrote a check to company. Did you pay them $8,353.76 or did you pay them $5,547.65? The amount that you actually paid to the company is the amount of your repayment. It doesn't matter how you or they calculated the amount, or whether, in your mind, there is some adjustment for taxes.
Let's put off any further discussion of what to do until you find out whether the company will be issuing a W-2C for 2017 or making an adjustment for the repayment on your 2018 W-2.
