I am dealing with this same issue. A customer paid online through QB payments. For reasons unbeknownst to either of us, the payment was rejected. They gladly repaid using a paper check. I deleted the old invoice, recreated a new, applied the correct payment, yadda, yadda, yadda. I have followed all correct bookkeeping procedures so my books aren't out of whack but the alert will.not.go.away. Sometimes, QB has really simple things that just annoy the crap out of us. Like little pebbles in our shoes. Except those are easy to fix!