The experience of a few (lots) of people who were overpaid and then badgered into writing cheques to repay the money, only to then find that JPA also reclaimed the same funds back the following month is v bad.
If you have had an advance of rates there is no system within JPA to balance the advance against the full claim. PMA have a growing list of people who owe money back which will be reclaimed "sometime"
Keep the money safely,
don't spend it because its recovery will be effected at this "sometime" future date.
If it is a 'simple' overpayment the system may reclaim it at the following pay period, unfortunately you then enter the JPA pay merry go round and, similarly to the old system, it will be months before it balances properly.