Hi! 

I am experiencing the same issue and I was able to match our received payments when the deposit hits our bank transaction feed. However, it looks like there is no way to match a refund receipt. So I created an expense with the resolve difference feature. But like you mentioned, the expense is not hitting the customer's account. Did you ever get a response to your question?

The system seems to work great except for this detail not showing up in the customer's profile.