As I understand, when we swap the slot, we can choose which appSetting key value to be stayed, but if the staging slot got the new key value which is not in the existing production slot web.config, how can we map the new key value in production web.config transform when we swap the slot?
Web.config transform and Azure App Service slot swap
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I am not sure if I understood your problem, but you can mark the AppSetting-Keys as "Slot Specific" or something like that and in this case they will not be transfered to another slot on swapping. Look here for more detailed description: https://learn.microsoft.com/en-us/azure/app-service/deploy-staging-slots