Select Bonds on the left menu of the Tenancy, then Prepare to Refund.

Enter the amount to refund the tenant, and the amount to transfer to the owner:

If the tenant is receiving a refund, update the Tenancy Invoice Contact with payment method and, if applicable, banking details, then run a Disbursement using a profile which includes Bonds.  The bonds to be refunded will appear on the same page as bonds to be lodged, in orange text so that they look different.