The relocation pay was required to be reported on his W-2 in 2019, and was subject to income tax and social security and medicare withholding. You are correct that it should have been reported in 2019, but you are not really out anything if you pay the tax on the bonus in 2023 instead of 2019.
What you are really looking for is a way to get the bonus tax-free because of the employer's mistake -- you don't want to pay this year, and you also want to argue that it is too late for the employer to amend a 2019 W-2.
For 2023, you would have to use a substitute W-2 form 4852. Enter the data that you believe is correct. In other words, substract $3000 from box 1, box 3, box 5 and box 16. Don't change the withholding in box 2, 4, 6 or 17, because that's what was really withheld. You may be asked to provide an explanation. (If you already filed your 2023 return using the original W-2, you would have to do an amended return.) Save copies of letters and other documents proving the situation in case of audit.
Note that Turbotax will warn you that you had too much social security and medicare tax withheld. There is nothing you can do about that in turbotax. to get a refund of those taxes (about $230) you would have to file form 843 by mail. This form is not part of your tax return and is not supported by Turbotax.
https://www.irs.gov/forms-pubs/about-form-843
Then, you have to hope the IRS does not try to collect on the wages from 2019, or if they do, you will have to cite the 3 year statute of limitation. The IRS can only assess tax (in most cases) for 3 years after you filed. So as long as you filed your 2019 return on time, the statute of limitations ran out in May 2023.
https://www.irs.gov/filing/statutes-of-limitations-for-assessing-collecting-and-refunding-tax
