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and with root permissions as i should do, neobackup needs it and on the job profile it is not installed root
I think you'll need to give root perms to the Shelter profile.
I'm not sure how to do that, maybe need to install Magisk manager there (again, share the APK via Syncthing). I assume since your phone is rooted, Magisk Manager will see that and be able to grant root to this profile too.
Though if you're rooted, you can just copy stuff to the Shelter partition. Each user partition is labelled numerically, storage/emulated/0 is the first user, so your first Shelter profile should be storage/emulated/1
Edit: Interestingly, my work/shelter profile is emulated/11