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I'm glad you visited us today so we can sort things out for you!
It's possible that the sales order is not connected to the invoice that's why it is still showing up. We can verify this information by checking the Transaction History Report.
To run the report, open the Sales Order, then click the Reports menu at the top and click Transaction History. This will show the Invoice attached to the Sales Order.
Once you've verified that the Invoice created was attached to the Sales Order, we can manually close the latter. Here are steps that'll guide you through:
After doing all these steps, the sales order will stop showing up. If you have questions, don't hesitate to let me know. I'm only a comment away.