Welcome to the Community, @jd34mx. Thanks for being so detailed with your concern. I'm here to help you rectify the transactions sitting in A/R unassigned. 

As an insight, the invoices are marked as paid after your customers send the payment using QuickBooks Online Payments.  

Since only open invoices will show on the Banking page, we can match the bank transaction to the payments instead. Here's how: 

1. Go to the Gear icon, then select Account and Settings. 
2. Select the Payments tab and go to the Chart of Accounts section.
3. Review and ensure that the payments and fees are deposited to the right account, then click Save and Done.

If these transactions were added and categorized as A/R, we can undo them first to move them back to the For review tab. Then, let's exclude them to avoid duplicate entry. Here's how: 

1. Go to the Categorized tab on the Banking page. 
2. Locate and select the deposits you'll need to exclude.
3. Click Undo in the Action column. 

Once done, go back to the For review tab and select the transaction again. Then, select Exclude. 

Also, if it's a single existing entry in QBO, it won't match to multiple bank entries. You can check out this article for the detailed steps on how to handle this situation by combining multiple transactions to a single record: Record and make Bank Deposits in QuickBooks Online.

Let me know if you have additional questions. We're always delighted to help you some more.