Maybe you should install it that way then. By default it would run as SYSTEM, get good local access, and not suffer from being suddenly killed by logging out of the account that a non-service Duplicati would use.
Duplicati Tutorial 02 Install Duplicati as a Service is one recipe (but not the only one), but for a new install.
Migrating from User to Service install on Windows are directions for migrating your current backup config which I guess is still giving warnings? You didn’t really say what’s going on, beyond not getting all the files.
To see the details of the warnings, you can watch About → Show log → Live → Warning. Possibly many are access permission errors. Maybe some are locked files, but a service could turn snapshot-policy on.
The logged in user that works the Duplicati UI web browser won’t matter any after you set up the service. What matters to get file access is the user that Duplicati runs as, and Windows is going to insist on that.