What do I do if deposits were never matched to the invoice payments and can't be matched at this point?

Welcome to the Community, @Kelsie504. I'm here to help ensure you're not keeping duplicate transactions in your books. 

First off, let's run the Transaction List by Customer report to verify the duplicate transactions. Here's how: 

1. Go to the Reports menu. 
2. Enter Transaction List by Customer and select to open. 
3. Set the date range in the Report period, then click Run report. 

Once confirmed, that's the best time to delete it. Just ensure they're not marked as R (reconciled) to avoid messing up with your reconciliation. Here's how to delete a transaction:

1. Open the transaction.
2. At the bottom, click More.
3. Choose Delete, then click Yes to confirm. 

As an additional insight, the downloaded transactions should match the ones you've entered in QuickBooks. To consider it a match, ensure that the amount of the bank transactions should be the same in QuickBooks, and within 90 days of the transaction date. 

Check out this article for more information: Categorize and match bank transactions in QuickBooks Online. It gives you better options on how to manage your bank transactions moving forward.

Feel free to message again should you have more concerns about anything else. We're always delighted to assist. 

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