Welcome to the Community, benj. We're glad to have you in this forum. You can manually update your bank feeds to ensure your transactions appear in QuickBooks Online (QBO). I’ve got the steps for you below.
QBO refreshes bank feeds automatically every 24 hours, though the timing may vary. This process imports cleared entries, making them available for review and categorization.
Since you're unable to locate it, here's how to perform a manual update to get your latest financial data:
- Select Transactions.
- Choose Bank transactions.
- Click the Update button.

On the other hand, QBO will automatically mark the invoice as paid once the funds are received if you're using GoCardless. The payment is categorized under Undeposited Funds, and a deposit is then created to transfer the amount to your bank account.
Since the system manages these entries automatically, you can find them in your bank register. Be sure to set the filter to ALL to view all relevant account data, as shown in this image:

With the information above, you should be able to locate your payment transaction in QuickBooks Online. If you have other related queries, please reply below. We're always around to help. Have a great day!