I'm having the same issue, and spent the same hour or so with customer support. I received largely the same response. But in very garbled English:
Regarding the refund for the check this will be successfully reverse when the time sent to that invoice meaning to say the date has been past , now what we can do is internal agreement with your customer end and for the recording to your QuickBooks online you can records refunds receipt for and attached the invoice of payment received.
When I told the rep that I did not understand what he was saying, he tried again.
Now you need to reach out your customer that you will be deposited back the check , this transaction is internal agreement . Then if you deposited back that amount to your customer , please kindly go to your QuickBooks Online for recording the transaction , go to +New > Refunds Receipt>Create make sure all information are the same or you may attached the invoice payment
In the end, after I tried to clarify "so, this means that QBO will process the refund" he said that no, we had to do it. Which he could have told me in the first five minutes in lieu of wasting my time explaining how to issue a refund receipt. Because, clearly, if a customer is waiting for a refund, what REALLY bothers them is the receipt.
In short, an hour of buzzwords in lieu of plain (and comprehensible) English to the effect of "no, Quickbooks cannot process refunds of e-checks; you'll need to do that manually yourself".
I have other clients with Stripe. Somehow, they manage to process refunds. I wonder how that is.
