When you setup RemoteApp in Azure Virtual Desktop – Microsoft has designed it to minimize the load of:

• The Run registry entry
• The RunOnce registry entry
• The startup applications

Simply to make a better and faster experience on the logon phase.
Read more about this.
The 2 workarounds Microsoft suggested in the above doc was not good enough for me.

In my case I needed to load another Windows Theme – as the theme in Windows 10 and 11 was bad for the legacy application like Microsoft Navision.

In my AVD image I created a custom folder with my scripts – C:\Windows\Customfiles\Run_Navision.cmd
When I created the RemoteApp in Azure – I simply pointed to the Run_Navision.cmd file that loads the new theme and start the application.

With this solution I am also sure it always run – no matter what new session host user joins.

Icon path is still to the Navision executable(finsql.exe) – to have the right icon in the Remote Desktop app.

Hope this helped you – enjoy!