I too went round and round with "support" and got nowhere! I was able to fix this issue this way:

Follows steps 1-4 here: https://quickbooks.intuit.com/learn-support/en-us/help-article/banking/handle-rejected-failed-bank-t...

Delete or VOID the new invoice you just created that you linked to the payment. The warning message will now disappear but your A/R and bank account amounts will be off.

This will give your customer/client a credit balance and your funding account (checking) will be credited in the amount of the reject.

Expand the "Refund a customer's overpayment or credit" at bottom, and follow steps 1-2 here: https://quickbooks.intuit.com/learn-support/en-us/help-article/customer-refunds-credits/record-custo....

In the expense, make sure to put the correct bank account (where the reject occurred) for "payment account" and the category should be "Accounts Receivable A/R", the preexisting AR account. 

Step 2 outlines tying the expense to the payment to zero out your client credit. 

This is totally ridiculous but it worked for me.