When you apply an open credit to refund you have to select either Cash, Check or Credit Card.  Unless you were in setup mode it should have posted to the general ledger.  Run the GL journal report for the date you did the application of the open credit.  If you do not see a journal entry then I would contact support at (800) 447-5700 and have them take a look at it.

The GL report shows, credit to cash and debit to AR. Should I do a Journal entry from AR to AP?

The GL report shows, credit to cash and debit to AR. Should I do a Journal entry from AR to AP?

If the GL entry shows it credited cash then you dont need to make any entry in GL.  It already made the entry.  If it does not show the entry in the bank rec you may need to do a CM bank transaction and deselect the post to GL to get it in bank rec.  According to your last post it did post to GL.