Depends on whether anything was done to disable it after moving to the service, e.g. is it still on the Desktop? Although it’s rarely a useful configuration, it’s also possible to run several copies of Duplicati at the same time.
Migrating from User to Service install on Windows calls for moving enough files that it should prevent the non-service version from starting, however if files were copied, and old desktop shortcuts and automatic starts left alone, then the non-service version may remain fully functional and run whatever backup was configured in it.
If someone wants the Tray Icon, the How-To calls for adding --no-hosted-server to its shortcut on the Desktop.