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So, if I understand you correctly let's say for instance that you earned $1,000 but were only paid $750.
So, you received $750 dollars and were taxed on that $750.
Then, your boss realized that she didn't pay you the other $250. So she'd make a check for $1,000 tax you on that full amount, then give you the difference between that net pay and the net pay she gave you.
This would be correct. She's not actually taxing you twice. It is actually more correct than cutting a check for $250 and withholding taxes.
She's not keeping the tax twice from you, she's just adjusting your pay so that what is withheld is correct.
Do you have any questions about this matter?