Error: Payment method is being using by a published or scheduled to be published store. Please remove it from the store and retry. When attempt to update a payment method.
First the payment method will need to be disabled on your Stores then you can update or make changes.
1.) From your Spirit Sale dashboard go to Store Fronts --> Stores.
2.) Scroll down the list of stores and look for a store that has the payment method enabled. This will be denoted by the logo within the Payment Methods box.
3.) Click the edit button (button with the pencil) to edit the store
4.) Under the Store Details tab, scroll down to Payments Methods. Stripe for example, if enabled, will be highlighted in a green box. Click the box and it will turn gray. This means the payment method is turned off for the store.
5.) Click the green Update button to save changes.
This process would need to be done for each published store that the payment method is enabled. After the payment method is disabled in all stores you can go to Settings --> Payments Methods. Now you can make changes to the payment method. The payment method can be reenabled on stores by following the steps and turning it on at Step 4.