That is not an amendment issue. You will have to work with the company.
You must confirm that the $400 was credited to you on your W-2, and that it's still included.
If the $400 is not on the W-2, the company owes you that money.
If it is on the W-2 you should get it back in your tax refund.
Then make sure the $1000 is not included on the W-2.