Integration between command line and web interface #2693 explains how
The commandline interface is intentionally separate from the server. The use case is for people who prefer headless commandline tools.
but this might open up the possibility that your server picked up the new version, while commandline did not.
C:\Program Files\Duplicati 2>Duplicati.CommandLine.exe system-info
Duplicati: Duplicati.CommandLine, Version=2.0.4.5, Culture=neutral, PublicKeyToken=null (Duplicati.Library.Main, Version=2.0.4.5, Culture=neutral, PublicKeyToken=null)
Autoupdate urls: https://updates.duplicati.com/beta/latest.manifest;https://alt.updates.duplicati.com/beta/latest.manifest
Update folder: C:\ProgramData\Duplicati\updates
Base install folder: C:\Program Files\Duplicati 2
Version name: "2.0.4.5_beta_2018-11-28" (2.0.4.5)
Current Version folder C:\ProgramData\Duplicati\updates\2.0.4.5 beta
shows how my 2.0.3.12 base version got to run 2.0.4.5 when the base version found and loaded an update.
Update locations vary, sometimes even being related to the home directory, which gets awkward if Duplicati happens to normally start as service/daemon as different user than the user running at a command prompt.
Downgrading / reverting to a lower version shows some of the places that the updates folder may be found. Did commandline find the spot? I think Linux also has a ~/.config/Duplicati/dbconfig.json file. Not certain if it might have some effect on this. I think @JonMikelV knows it better, so I give this back after interrupting. 