Thanks for your question,
If you configured AGIC, the Application Gateway is now managed by the AKS cluster and you should not create listeners manually in the Application Gateway:
"With default settings, AGIC assumes 100% ownership of the Application Gateway it's pointed to. AGIC overwrites all of App Gateway's configuration. If we were to manually create a listener for prod.contoso.com (on Application Gateway), without defining it in the Kubernetes Ingress, AGIC deletes the prod.contoso.com config within seconds."
All the listeners and configurations are created by the AKS Resource Provider, according to the ingress you create on the AKS cluster. You can further configure the App Gateway via annotations on the Ingress object, those will also be applied by the AKS RP.
The manual changes done in the app gateway will be undone by the AKS RP shortly after.