BTW the pharmacist in charge has a way to override, the prompts of the "not picked up" report. So Dej, the insurance will be billed probably. The pharmacy will get paid for the medication but will lose any copay from you owed if you were not scanned out properly. It will not be a total loss, for them. The payment is figured by wholesale cost + a dispensing fee... from the insurance. The dispensing fee is quite small but something.

It is not any different from refunding a copay for an error.

One thing bothers me about this though. A manager can recall transactions from the registers these days. All the large companies now have that computer capability. They use this feature when someone tries to get refunds on purchases (non pharmacy without a receipt). Perhaps you've seen it in action? They can even print out a duplicate receipt (say for a rebate if you've lost your receipt and want another).
Now I don't know if your pharmacy is some small mom and pop?
If it is that might be not available. But RiteAid, CVS, and Walgreen's should all be able to find the transaction and see for sure if you paid for the RX.