Well from a tax perspective the wages for those 3 days were already paid even though she did not work them. So she has been paid for 3 days as if she had worked them. I would just take the gross pay for those 3 days and reduce them from either the final paycheck or severance package. Nothing changes from a total wages paid perspective in that case. If I forgive the days, then it just gets added to her final wage calculation.

They were not taken out of the paycheck when they were used because they days were not taken as unpaid. They were taken as PTO when no accrued PTO was available. If she worked for us for another 3 months without taking a day of PTO, she'd earn all of those days back.