@smpri 

"Right now, my bank account is reconciled (excluding that payroll item) and the employee has the proper withholding, but there is a discrepancy between my bank balance and the balance in Quickbooks."

Ahh, got it.  Since you need to fix this in the current period and your withholding is/was correct, the fix is to make a deposit in the current period and assign Payroll: Wages to it.  That reverses the effect of the $100 payroll check never given to the employee - it increases your bank account by $100 so you can clear that against the $100 payroll check the next time you reconcile your bank account and it reduces your Payroll: Wages by $100 because that's currently $100 overstated.