I deployed two .NET sites as Web Apps (PaaS) in Azure that were running OK for several weeks but started having issues and have now been stopped for investigation. The problem is that some additional "phantom" instances of my applications keep sending messages to my logging server.
These phantom instances also seem somehow corrupt, as they keep restarting every 5 minutes (due to Always-On?) and then report of problems during startup that don't affect the "normal" web app instances. For example, one app reports that it cannot find a path, which does exist on the Web App VM (verified through the SCM web interface).
In summary:
Why and where are these erroneous phantom apps running and how can I get rid of them without recreating new Azure web services from scratch?
Based on your description, you have stopped the Azure Web App, but seems the web app still send messages to logging server? If so, I would suggest you use Resource portal to stop the Web app, we can sign in Azure Resource portal, then find your web app, set "state" as "Stopped", and "enabled" as "false" (We can use this way to full stop the web app). Then check to see whether the Web app can send message to logging server.
due to Always-On?
By default, web apps are unloaded if they are idle for some period of time. If the web app is stopped, the Always on will not affect the site.