John, like you, I do the books for a non-profit. QuickBooks online does not have a good way to handle returned/ bounced donations. I had also done the simple journal entry as you suggested. However, the donor's account is only affected if you use accounts receivable, which throws off your accounts.

The original donation had gone to an income account, so I made the debit to the income account and the credit to the bank account that the original deposit hit. I had entered the donor name and the appropriate class. But QuickBooks did not change the donor's account. So the accounts will be right, but the donor will show as having given money that did not actually clear. Then when the replacement donation hits, it will look like he gave again. You can't do any sort of negative donation, voiding, or otherwise accounting for the customer's /donor's portion. 

Any other thoughts, or ideas?