Thank you for reaching out to us. As long as you have selected the option Automatically update super rates on your Payroll Settings, it will automatically update every time a change is made to the super rate. Can we try to click Actions > Recalculate, or you may delete and recreate the pay run if it has not been finalise yet.
I hope this helps. If still it doesn’t work, I'd highly suggest you contacting our QuickBooks Online Support on this link so they can check further: