I have created an App Stack for an application we use called Phoenix. The stack mounts and works properly however I need to enable a feature in the application called remote job execution. When I build the AppStack the XML file containing the remote execution settings is created and placed in the AppData folder of the account I use on the capture machine. When I log in to test the app stack the file does not exist therefore the application runs but without the remote execution parameters. We are using mandatory profiles for the pool where the app is being used and the AppStack is mounted after the profile is loaded.
It has been noted before on this forum that user information is not stored in the appstack. So Appdata of the user and HKCU is not recorded and information in these 2 locations will not be in the appstack.
You could try adding it to the mandatory profile or adding it to the C:\Programdata folder.
Otherwise you will need to use either GPO, UEM or the .bat files in the root of the appstack to execute a copy command from the file to the APPDATA folder.