Draft Regulation 147J of the Income Tax (Pay As you Earn) Regulations 2003
If an employer overpays the Apprenticeship Levy, the resulting credit will be dealt with in the same way as any other PAYE credit. If they have any outstanding employer liabilities, it will be used to clear those liabilities with the oldest being cleared first. We do not tell an employer when money is reallocated - they should review their online PAYE account to see the current charge and payment position.
If there is still an overpayment, then we recommend that employers reduce their next PAYE payment so that they don’t have to contact us to arrange for a repayment. For information on claiming a refund , employers can go to https://www.gov.uk/payroll-errors/correcting-payments-to-hmrc