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For anyone else that comes across this issue - I resolved it by adding the `WEBSITE_RUN_FROM_PACKAGE` app setting to the app service with a value of `1` in Pulumi. When deploying code through VS/Rider/deployment task in ADO/GH, this setting is automatically added to ensure the application is ran from the packaged version that exists on the app service file system.

As this wasn't defined in Pulumi, it was being wiped, along with the application files, leaving an empty app service.