@Mohamed Chibani Thanks for reaching out.
As per the app configuration pricing document here the pricing is for per day for both cost per store and cost per replica. If you delete the instance, then you will be charged according to per day usage of your app configuration based on the how many stores and replica you have used.
Once you deleted the app configuration you will not be charged further, and the billing for app configuration will be stopped till the day cycle ends on the day of deletion of app service resource.
Let me know if you have any queries or concerns.
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