I appreciated all the steps you've done and for outlining the complete scenarios of your concern, mkm2.

I have here some details and instructions on how to resolve the customer's negative balance in QuickBooks Online. Rest assured, that this reply is not about entering a refund and their links. 

Let's double-check the customer's transaction in the lists. Make sure that there are no outstanding transactions and credit so the negative balance will fix. If there are, I'd recommend deleting it so your reports and accounts are accurate. 

Here's how: 

1. Go to the Transactions List on the Customer page. 
2. Click the Filter drop-down arrow, then choose All transactions and All dates. 
3. Review each transaction type. 
4. Click the transactions and tap Delete under More. 

Once everything is set, you can always run any customer reports to track all the data you've entered into the system. You can also customize and memorize the reports. You may refer to this article for the detailed steps: Run reports in QuickBooks Online.

Lastly, feel easy to check out these articles below about handling customer's transactions, banking data, and reconciling accounts.

• Reconcile an account in QuickBooks Online
• Banking
• Sales and customers

Post again in the Community if there's anything else you need or follow-up questions. I'm here to keep helping. Keep safe, mkm.