I’m not sure how you migrated to a service install but it seems like a step may have been missed, I’ll address this in a minute.
For now the dbconfig.json. The dbconfig.json gets created in the current users local app data folder, so in my case "C:\Users\Jimbo\AppData\Local\Duplicati". FYI: None of the database entries in the dbconfig.json file I have match up to any of the database names I currently have.
I don’t know what the dbconfig.json does but I’m pretty confident you don’t need to worry about it either.
My databases are held in "C:\ProgramData\Duplicati\Data" which contains three databases (I only have 3 jobs setup), EBTCIBJAKH.sqlite, MFSTBPUEDJ.sqlite and UEVBRQUEKO.sqlite which matches up to the WebGUI when I select a backup job and click on “Database…” I see the same database name.
As for Duplicati being setup to run as a service in Windows, I would suggest trying to follow this guide. If everything goes as planed your databases will then be located in "C:\ProgramData\Duplicati\Data" and if you check your services you should have a Duplicati service running and the “Path to executable” in that services properties should read "C:\Program Files\Duplicati 2\Duplicati.WindowsService.exe" "--server-datafolder=C:\programdata\Duplicati\Data"
The "C:\Windows\System32\Config\SystemProfile\AppData\Local\Duplicati" folder should have been removed when you migrated to a service install. Also I have a post a further down in that thread explaining to add the --no-hosted-server option to all of the shortcuts that launch Duplicati along with adjusting the source selections so they are system based and not user based.
Once you know for sure what databases you’re using things should be much easier to diagnose. Let me know if you have any questions.