Ok, so our app can't stop your old/pre-existing rates from showing up.
Any rate connected to your shipping zone has the right and privilege to show rates without interference from our app.
Your pre-existing rates are setup to always show without conditions.
If you want them to only show, under conditions, like don't show when our app is showing rates, then you need to re-configure your pre-existing rates into our app within the default group. And then remove the old rates manually.