I can share why you can't select an income account when matching the deposit to an invoice in QuickBooks Online (QBO), northamptonfrien.

If the item or product on the invoice you're linking to the deposit is already assigned to an income account, it will be defaulted to that account when matched. That's why you no longer have the option to select an income account when associating both data.

On the other hand, it's not advisable to make another deposit to link to the existing invoice as it would double your income in your accrual Profit and Loss. Since you're using the QuickBooks Payments feature, once your customer pays the invoice, the balance and status of the invoice will be marked as Paid. 

Furthermore, all that's left to do is to match the downloaded entry to the generated payment to clear the transaction.

Finally, you might want to ensure your transaction in QBO mirrors your bank statement. With this, the reconciliation feature in QBO can aid you in reviewing if you have accurate data. It could also help discover any discrepancies in your transactions.

If you have follow-up questions about matching or categorizing your bank feeds, kindly post them in the Community forum. We're available 24/7 to lend a hand.