If you wish your database to be moved (and you have a GUI install, which was made after the CLI version),
Database management has a Location section with a Local database path you can edit, and the Move existing database button will become active (shown in blue), and you can click to move and remember.
Testing I just did suggests that if you set up both the Database screen and dbpath in Advanced options, the advanced option wins. If you are running from the CLI, there is no Database screen so it can’t conflict.
Your result sounds different though, but your release may differ, and some wordings are a bit ambiguous.
Can you please make a table or description of what you have for the 3 backups, showing C: or D: in GUI Database field, and which file is actually updated by a backup. I assume the dbpath is a unique path on D: for each backup, given in the backup Options screen. The Settings screen would be for default options.
If you wish to stay off of C: for everything including Duplicati-server.sqlite that holds information for the GUI, –server-datafolder option on the Server or TrayIcon launch can do that, or set DUPLICATI_HOME variable. There’s an easy way to set that up shown here, but I think you’re on your own to move any active files over.
Files that haven’t changed after all backups are run aren’t very interesting. Some may have backup in their names, and many of these are only useful short-term, or maybe for emergency work if active file gets lost.
The dbconfig.json file is relevant to CLI, and tries to remember things like DB location for destination URLs.