The cause of this problem is the config attribute nsslapd-parent-suffix
was not defined as an attribute of DN syntax. Because of the missing
definition, the value is not the target of the DN normalization and
the match fails after upgraded. Adding the attribute to the schema
solves this problem.
Plus upgradedb does backup the DB before upgrade, and if it fails
it restores from the backed up DB. Use dblayer_restore instead
of copying DB files one by one.