I did a partial refund the other day (full cost of item, but I didn't refund the postage), through PayPal. That said, my buyer didn't open a dispute either, they just sent me a message and we sorted it out via messaging. She didn't ask for a refund as she was still really happy with it, but I gave her one anyway because the item arrived broken (I asked for a photo, which she sent). I obviously hadn't packed it well enough, so I was happy to shoulder the blame.

Maybe you can't do a partial refund if a dispute is open?