Even with a $0 order for free tickets, you can process the order as a regular refund to mark the registrants as canceled and add the tickets back to your event's inventory.​
  1. Go to Sales > Refunds
  2. Search for and select the order
  3. Note:  If you only need to refund some of the items in the order, only mark the check boxes next to these items. 
  4. Click Refund
  5. A pop up box will ask you "With this refund, do you want to mark registrants as Canceled and add tickets back to inventory?"  Click Yes