Hi @purplesalix
There's two options here.
1. With multi-currency support
If you have multi-currency enabled, you can go into the original invoice, create a credit note and mark that as the correct amount and paid from your bank. Remember to delete the original bank transaction as it would now be duplicated.
*2. Without multi-currency support
If you don't have multi-currency enabled on your account, you could create a negative purchase. Simply create a new purchase but enter the amounts as minus values. This will prompt you where to refund it to, and you can select your bank account. Again, as above, remember to delete the original transaction as it's duplicated.
I hope that helps! 