Sorry to say I do not fully understand your issue. Could you please elaborate on your concern more with some useful screenshots so that we can better understand and assist you accordingly with the issue you have faced?
Also, share the wp-login details of your site so I can check and give you a possible solution.
I have added free shipping above a certain amount, but it shows me both options at checkout! We want the other option to disappear when the amount for free shipping is reached.