For anyone who has spent half a day tearing their hair out over this (like I have, 4 calls to QBO help line later and still no resolution!), here is the solution I used that cleared the dispute message for a bounced payment:

1. When the bounced payment withdrawal is taken back out of the account, create an expense using the customer's name and the accounts receivable account to match to the withdrawal.

2. Change the payment that later bounced, to match to the new expense. The original invoice will go back to showing being due.

3. Once the bounced payment is resolved and final payment is made, match that payment against the original invoice. 

All four of these transactions show under the same customer and at this point the error message has disappeared, my BS and P&L are accurate, and I can finally go take a walk

Best of luck!