Windows version upgrades (not monthly updates) move Duplicati from SYSTEM profile to Windows.old, which isn’t great (especially if you don’t notice before Windows removes that folder). For a service, safer places for Duplicati config use Duplicati.Server.exe options --portable-mode or --server-datafolder which you can add by editing the service in Windows, or pass as Duplicati.WindowsService.exe options.
This is odd though, although details are scarce. If it was a Windows wipeout, you’d lose the configuration.
Downgrading / reverting to a lower version talks about locations. It sounds like your service is likely using C:\ProgramData\Duplicati, but if you start Duplicati as you logged in, that’s the one in the user profile.
Sysinternals Process Explorer shows what executable image a process is on if you mouse-hover over it.
Task Manager can probably do this if you select an Image path name column. Duplicati processes often come in pairs, with the initial launch from Program Files, then child on whatever’s the latest update found.