Tray icon Service Mode [WINDOWS*

I think so. Backup database paths (and all other job settings) are in Duplicati-server.sqlite:

Going underneath Duplicati to move Duplicati-server.sqlite does not edit job’s DBPath above.
That would need a separate independent operation done by you on the job database screen.

Whenever you like, or never (if you don’t mind backup databases remaining where they are).
If you’re trying to avoid Windows update damage, best to leave nothing in SYSTEM’s profile.

Migrating from User to Service install on Windows did server DB first. Other order may work.
Please look at this How-To. If you’re now at moved-server-but-not-jobs, jump in at the below: