Addendum: I was also able to migrate my existing settings on a machine that already had Duplicati installed in service mode. I stopped + uninstalled the service, moved the data files to the new location, and reinstalled+restarted the service with the parameter that points it to the new location.
Unfortunately it then went a few days without backing up until I noticed. Turns out you have to also update the local database path in the web UI, or else it tries to access it in the old location and reports a locked file error (?).
if you export a job as command line, you’ll see in the --dbpath parameter that the server database stores an absolute path to the job database. In practice by default, the job databases are in the same directory as the server database, but it’s not necessary. So moving all the databases together is not enough.
The people migrating from user to service install found probably the same thing in v2 below.
It looks like v3 found out the risk of the current default location. So maybe you got both now.