The only way I know of to do this would be to create the credit note via the “more options” drop down on the original EUR invoice, which should allow you to set the GBP value of the refund. This will create a duplicate pre-tagged transaction on the relevant bank account, so you then need to delete the untagged one that came from the bank feed.
To my knowledge (I don’t work for QuickFile) there’s no way to link a credit note refund to an existing bank transaction, only to create a new transaction as above.
When the amount being refunded is less than the invoice amount, everything is easy and can be done through the standard refund option.
But when the amount being refunded is more than the invoice amount and I follow the proposed solution, the duplicated transaction is of a different amount, so I can’t just delete the original transaction in the bank account because they are different amounts.
you can create a stand alone credit note that equals the amount coming back to you. You would do this by raising a negative invoice. you will then be given the option for where the refund should be entered (this will generate the bank transaction so you will need to remove the original)
If you do it with a journal it’ll be right on your P&L but the transaction won’t appear in your VAT return (assuming you’re VAT registered) as QuickFile only uses sales and purchase invoices and credit notes for VAT.