I agree, it is clumsy but AR Voucher is definitely not the way to do it.  If you are receiving a check from a vendor, there must be a credit on their account in your AP Aging that the refund is paying off so you have to process through AP.  You record the receipt of cash in GL-B as a cash receipt, debiting cash and posting the credit to any miscellaneous account.  Then in AP-B enter a voucher posting the debit to the same expense account so they cancel out.  Then use AP-F and pick the credit and voucher and process a $0 ePay.
 
We will look into a less clumsy approach.