Configuration seems to have disappeared after reboot?

It would be worth a look at ~duplicati/.config/Duplicati to see what it has (ideally your config, etc.).
The historical issue with Arch is that AUR liked to run as a duplicati user (secure but complex).

Welcome to the forum @NBoumakis and thanks for the help. There might be related info at AUR:

Package Details: duplicati-latest 2.0.6.104-3

Previously I only knew of old issue, but the recent change with typo reminds me of things you said.