Hello Claudio
As you stated correctly, a payment can only be assigned to an open invoice.
It is possible to copy an invoice/transaction in the portal though and then connect it to the second payment via the "Link invoice button".
After that, the refund can be issued with the necessary steps. (Be aware of the difference between generic and Postfinance ISR)
This way, you can resolve the manual task too.
For details, please email info@wallee.com and link this wallee ask.