Continuing thread from
OSError: [Errno 2] No such file or directory: './erpnext/private/backups' - #9 by yashodhan as suggested by @yashodhan
I was only partially able to delete the base_vat app. As you see from the log above, there seems still to remain a dependency, which blocks any updates.
bench --version
4.1.0
bench version
erpnext 10.1.52
frappe 10.1.47