It’s not a good idea to use the built in command line if you intend to continue to use the web UI since it doesn’t really communicate with the Duplicati server. You’d need to repair your database every time you need to use the server to run jobs.
A better way to initialize the backups would be to have the cron job interact with the server web API to start the task. I made a script that can help with that 
As far as I know, there’s no problem running a backup job from the command line that’s exported from the GUI. Both can be used in turn without issues.
The only small backdraw I’m aware of is that the number of available versions showed in the main screen is not updated when run from the command line.
When using an external scheduler, the schedule in the backup job configuration can be disabled.
This video demonstrates how it works
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(btw your Duplicati client is great!)
Ah, of course, If you specify the dbpath it should work the same. Then yes, it’s just the metadata that’s wrong. My bad