From your link, would this be version duplicati-bin 2.2.0.0-1 from AUR team yesterday?
Someone else is reporting a weird bug (not this one) with that. Any idea of old version?
Warnings can persist over restarts, as they’re in server database. Did you ever Dismiss?
Another test could be to use known-bad --settings-encryption-key to see if it breaks.
I’m not much up on user service behavior. If needed, maybe test the same line from shell?
This tends to write errors onto the terminal. OTOH you might find yours in systemd journal.