I think, you should go directly to that invoice and in the More Option menu above the invoice you should click Credit Note. Refund the amount of the deposit and it will create a entry in your current account (in quickfile) Then you should go to your current bank account (in quickfile) and check that there is the new created refund entry. If you see this entry you can then delete the original entry submitted from your bank.
You can find more info here: