Azure App Service is a service used to create and deploy scalable, mission-critical web apps.
Thanks for asking question! It seems that the Custom domain of AFD and custom domain of App service are different.
Just to confirm have you setup custom domains on your app service.
Further if you are looking about AFD automatically configuring custom domain on backend app service then this feature is not available and there is ongoing feedback on this.
So as a workaround you need to manually register the custom domain by changing the CNAME record to each of the App Services in turn, and then point the custom domain back to Azure Front Door. This way both AFD and App service will have same custom domain and session affinity will work.
You may refer this blog might be helpful.
Let us know if further query on this or issue remains.
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