When refunding orders in Givecloud, you'll see the option to do a full refund versus a partial refund. When performing a full refund, Givecloud will automatically adjust all the linked gifts in DonorPerfect to $0 to indicate that a refund has been issued.
Be sure you check your DonorPerfect settings screen and enable "Auto-Sync Order Refunds".
For now, partial refunds still require manual adjustments in DonorPerfect. We are hard at work on better partial refund support that will allow you to identify which line items need refunding, and subsequently, which gifts will be adjusted in DonorPerfect. Keep an eye on your updates feed for more info in 2019.