To the best of my knowledge, a partial refund alone won't trigger a defect. (A whole refund via paypal without subsequently cancelling the ebay transaction may.)
I regularly give partial refunds for the specific purpose of refunding postage paid on multi-item orders that didn't combine shipping properly through the US Cart on ebay.com. (Or UK Basket on ebay.co.uk.) While I have a sneaky suspicion that either ebay or paypal watches for partial refunds as a sign that a seller might be troublesome, I don't think it alone has been proven to be an official method of evaluation.
If, however, your buyer leaves feedback that gives you poor marks for this transaction, there's nothing that can be done to eliminate that associated defect. The same goes for an Item Not Received point of contact or the like. If this matter had come to your attention through the Resolution Centre, you would be sailing the defect ship regardless of how you handled afterward. At least, that is the way I understand it to be. I have no personal experience there, although you may hear here from other members who are more knowledgeable in that respect.
Good luck as you carry forward.
w~~_7.JPG "pjcdn2005"){kind=avatar}
