https://bugs.openldap.org/show_bug.cgi?id=10277
--- Comment #1 from Howard Chu hyc@openldap.org --- (In reply to Ondřej Kuzník from comment #0)
If someone deletes a cn=config entry offline (or through bugs in cn=config, they exist, will file as I isolate), the X-ORDERED RDNs will not be contiguous. cn=config papers over this internally at a cost of never being able to modify the entries affected.
The files in a back-ldif directory comprise a database, no different from any other database. If someone mucks with the DB contents directly, instead of using the provided tools, then they've intentionally corrupted their DB, and that's all their own problem.