The only thing you would adjust for is any pre-tax deductions that would have reduced your W-2 box 1 income. To figure the credit using your 2019 return, you need to essentially guess what your W-2 box 1 wages would have been with the reduced wages. (Don’t change any other boxes on your W-2, just box 1.)
As an example, suppose your retirement is 5% pre-tax contribution and the TSP is a 6% pre-tax contribution. If you received a $5000 bonus in gross wages, $250 and $300 would have been subtracted per-tax, so your box 1 wages would have been increased by only $4450. So when you try to figure out what your 2019 box 1 wages would have been without the repayment, you will take pre-tax deductions into account but not after-tax deductions.
