You can’t.
If your OneDrive is not configured to do full sync, you shall exclude the whole OneDrive folder.
Duplicacy cannot materialize cloud-only files and so there would be very little reason to attempt to backup random subset of files that happen to be local that day, you would not be able to rely on such backup because you would not know if a specific file is there or not. It’s best to exclude the whole folder.
If you really do need to backup OneDrive contents, but you don’t want to sync entire thing, an alternative approach is to mount OneDrive with rclone, with a small local VFS cache, and backup that mount.
Unlike OneDrive, that uses reparse points and other filesystem magic, rclone relies on a virtual filesystem (or, in the recent versions, they added support for local NFS server, or you can use SMB too) where files are always appear present. This works very well with duplicacy and other file based tools.