The application settings persistence feature persists most files and folders that are contained in the Windows user profile. Per the documentation, that folder is C:\Users%username%. Note that some folders are excluded from being persisted (basically the user data directories).
The S3 Home Folder feature will only persist files and folders that are specifically saved to it. The Home Folder location is C:\Users%username%\My Files\Home Folder. Anything saved outside of this folder will not be persisted by the S3 Home Folder feature. Note that Home Folder mounting begins after the user session begins, so there can be some time after the application attempts to launch that the Home Folder is not yet available.
Since C:\appname is not included in the Windows user profile, or in the S3 Home Folder location, it will not be persisted. If you can move your application's files to either the Windows user profile (except one of the folders not persisted) or the S3 Home Folder location, AppStream 2.0 can then persist it.
Nothing you save in a folder off the C Drive like that will persist. App Settings Persistence is in the user's APPDATA folder, and Home Folders is an actual folder that you must intentionally save data to, it's not going to proactively scan folders as you are suggesting.
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