Did you set the service up to use the correct sqllite databases? I haven’t (yet) installed on Linux, but on Windows it uses different paths for the databases when installed as an app versus as a service.
It might work to just move them around manually. For windows, see Changed from app to service: backup no longer found
I think the key is to use --portable-mode so the databases are in the duplicati 2/data dir.
But again, I haven’t looked into this on Linux, I’m still working on protecting windows stuff via a service.