How do I removed Adv Pay Balance in payroll?

Do you use the preference setting to Copy Previous paycheck? In other words, in Paycheck Details view, left side, if you see something that you know is Not supposed to be there, you Delete that line.

"Also there is a side entry, that says Adv. Pay Bal $ -50.00."

Side entry when viewing What function? When an addition or deduction item has a limit and that goes to 0 = fulfilled, then the item stops computing, but still shows until you Remove it from being in use.

Edit Employee and delete this payroll item from their list of Payroll Activities, since it no longer applies.

It is not Controlled by the account balance. It is controlled by you.

Looks like perhaps no Limit was set on the Advance. Even though the loan has now been repaid in full, QB continues to take the deduction from the employee's paycheque (or did at least one time). Check to see if the employee's last check was short by $50. If so, refund the employee using the Advance item on the next check. Then remove the advance Item in the Employee's Profile.