I understand that you have two issues with debugging your app traffic.
Firstly, you could enable Fiddler troubleshooting from the Help\Troubleshoot... menu. This will show all sessions in Fiddler. The ones which should be filtered will have strickethrough.
The first issue is that you do not capture the push notification from the service to your app. If the troubleshooting does not help, what protocol the notification is send over? Is it a WebSocket, secured WebSocket or something else? If it is secured, you have to configure the https decryption.
The second issue is that Fiddler is not always tampering the response before it is send to the client. Could you, please, elaborate on how you tamper the response. Sharing some code will be best.
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