Hello Erika,
Thank you for your reply and attempt to help me with this.
I'm afraid I still didn't manage to resolve this, in spite your explanation.

This is where I am now:
- Duplicate payment done on 15.01. recorded as Expense with category A/P

- Supplier Credit created with the same date (15.01.) with the category same as for the original invoice we paid

- Bank Deposit created on the date when the vendor paid back the money (05.02.) using account A/P

Is this ok, and how should I proceed?