Installed Windows 10 Fall Creators Update - Now Everything is Missing In Duplicati

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I fully agree, but keep in mind that this is more an issue hat Microsoft should solve than a bug in Duplicati.
Duplicati stores all settings and local DB’s in the AppData folder under the user’s profile. Most likely this is a subfolder of C:\User\<Username>.

When Duplicati is registered as a Windows service, it will be started using the Local System account. This is not a “real” user account, you can’t log on interactively with it. This account also has a profile folder, but it is not located in C:\Users.
The location used to store the Local System’s profile is C:\Windows\System32\config\systemprofile. The environment variable %APPDATA% (this variable is used by Duplicati to choose its storage location) points to C:\Windows\System32\config\systemprofile\AppData.
This is why Duplicati DB files are stored in C:\Windows\System32\config\systemprofile\AppData\Duplicati if it is started as a service.

During a Windows 10 upgrade, the complete Windows folder is renamed to Windows.old. The installer tells that all user data will be retained, but it seems the Local System’s profile folder is forgotten. The contents of the systemprofile are not part of Windows, but contain most likely user data. So Microsoft should fix this.

There are a few workarounds you can use until Microsoft has fixed this in the Windows 10 Upgrade procedure:

  • Run the service in Portable Mode:
    Unregister the service with Duplicati.WindowsService.exe uninstall and re-register it with Duplicati.WindowsService.exe install --portable-mode.
    Duplicati will use the folder named Data under the program folder. Copy or move the contents from C:\Windows\System32\config\systemprofile\AppData\Duplicati to the Data folder under the Duplicati program folder (most likely C:\Program Files\Duplicati 2).
  • Specify a custom data folder:
    Unregister the service with Duplicati.WindowsService.exe uninstall and re-register it with Duplicati.WindowsService.exe install --server-datafolder=<path>.
    Almost the same as the first workaround, but you can specify a location outside the Duplicati program folder.
  • Start the Windows service with a “real” user account, preferably an account with administrative privileges. This will move the Duplicati data folder from the systemprofile folder to the user’s AppData folder, located under `C:\Users. Again, copy or move the contents of the Duplicati folder from the old to the new location.
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