The item in question is a service. Regarding the refund, I wrote a check and chose the the relevant item from the Item tab. In the past, these would automatically be applied against the revenue account. Interestingly, after saving I see the account listed in the check register is the COGS account. If I edit the check, I can still see that the correct item is being used and nothing is entered on the account tab. To fix this, I edited the register and chose the relevant income account. Since this is the FIRST time in recent memory that this has happened, I asked the question.