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Sue you can file an amended return any time after the original was returned.
On your other question, not sure I understand ... are you asking an accounting question? (how to get the funds off the w-2)
I'm guessing that you accrue the expense by making an entry like this:
Debit payroll tax expense 1000
Credit Payroll taxes payable 1000
So the entry would be the reverse of that for the amount that takes the payable to zero