Hi NickW,
You should use a 2nd bank account, a kind of holding account. If you don’t have one already then create one. This account is quite useful for other things too. What you need to do then is to tag the refund as a “bank transfer between account” and use your holding account.
Enter the amounts of your 3 invoices, which were refunded, manually (each as a separate line). This will/should balance this holding account. Then tag each line, which you entered manually, to the purchase invoices as a refund/credit note.
I hope this helps a bit.
If not, here is a similar thread: