Here was earlier a wrong answer. This is the correct one.
I guess you have a date selection too narrow.
1. Please select a beginning date back to where the supplier invoice was done, and the invoice should show up.
2. When you run the supplier credit note, you still have paid for the supplier invoice.
3. The money that came back can be returned in Bank Deposit. Select supplier and enter the correct bank and amount line.
This should do it.
But if you for some reason cannot get to the invoice lines you can try the following:
1. Deactivate the allocation from the payment.
2. Go into Purchase tab. Click 'Allocate Supplier Payments or Credit Notes'. Click 'Show Settled Items'. Now you see your initial payment. Click the money note to the right and remove the amount allocated from the invoice. Save.
3. Now you have undone the allocation. Now you can credit the items. And finally you go into bank deposits and select your supplier. Enter the payed amount you got back and everything should be ok now.
It is a little bit tricky when the allocations have been done. Had there been no allocations everything had been strait forward.
Joe