When we have the store running with some payment methods and we decide to change some method, for example, add Cash on Delivery or remove Stripe, we must change it in our private area. In this way, the orders that enter with the new changes, will enter our system correctly.
To do this you can follow the same steps as when you set up your store, only you will have to modify, add or remove what you need.
You can see the steps in this article: How to activate your store