If IRS is not crediting you with box 2 withholding you have to dispute their changes.
If the IRS letter doesn't tell you how to fix the problem,
you should reply saying you are going to amend and report the missing/correct federal tax withheld.
When you amend you have to include copies of both W-2s showing Federal tax withheld, and any other tax documents that show federal tax withheld.
This is not rocket science.
