QB customer service claims that you can not refund a eCheck, here the original response:

Thank you for patiently waiting. So upon checking here, we can no longer reverse the transaction. Therefore, what we can recommend is to come up with an internal agreement between you and your client to either have this money returned through cash or paper check. You actually have the option to reverse/refund the transaction to your client on the same date. Before 3:00 PM PST.

Customer representative: [Removed]