If your friend contacted his bank and they investigated the charge, they should have told him why they believed the charge was authorized. He placed a claim, we assume, for an unauthorized electronic funds transfer. The problem is, you say he signed the sales slip.
While he could contact the banks regulator and file a complaint, there may be a better way to go. As you mention, the business should have settled its books and had an overage. Their cash register shouldn't have balanced that day. The skeptical side of me says that if your friend spoke to someone at the business, how reputable are they and could someone have taken the cash so they did balance that day. It could have been a bad employee, or they could maintain they gave the cash to your friend. The business manager/owner should be contacted and if your friend wants to pursue this, the Better Business Bureau may be the next stop.
The longer this goes without being resolved the harder it will be to get that money back.
_________________________
AndyZ CRCM
My opinions are not necessarily my employers.