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Glad to see you again in the Community, @Bazinga.
Currently, there isn't a way to remove these balances directly from the bank feeds. You'll need to link the payment deposit to the open invoice to clear up the zero net balances.
Next, apply the deposit entry as an invoice payment:
This should get you on the right track.
For other bank feeds issues you may encounter, you can use this link as your helpful guide: Bank Feeds in QuickBooks Desktop.
Let me know if you need anything else. I'll be around to help. Take care and have a good one.