Hi Desley12
Welcome to the Community Forum, I hope you find it a valuable resource.
The idea is what's recorded in the software should match what happened in real life. Since the first $1000 was refunded to your bank account, the software can also reflect that by having a supplier return created by creating a new $0 bill with amount paid, or record supplier payment against a closed bill, either way will create a supplier return. After that you can go to Purchases > Supplier returns to refund it, this refund received matches the return on the bank statement.
Please feel free to let us know how you go, or if you have any further questions.