Looking at a virtualised application process, and it tells me that the path is %LOCALAPPDATA%\Microsoft\AppV\Client\Integration\76BAA2C3-BA7E-42EA-A8E3-5B7176CE7B40\Root\syst\MyApp.exe
But that I really want to know is "Is it the application which thinks it's c:\program file\mystuff\syst\myapp.exe And there doesn't seem to be any way of doing that.
Is there a Powershell command that will tell me that?
From what I know this not something you can do, this is because of how App-V and other similar technologies work.
They work by hooking into the system using the Filter Drivers, based on APIs provided by Microsoft. Those filters allow the App-V client to place itself between your application and the OS and redirect the calls, for files and registry paths for example.
So in theory, for an application to be able to read the real paths your app is trying to access it would need to have a higher filter altitude allocated than that of the App-V client, that capture and read the calls before they get to the App-V client.
To get a better image of how filter drivers work in App-V I highly recommend the following video, where one of the founders of the company that created App-V explains it with details: