we have told it to syncrepl from scratch into an empty directory.
Catastrophically bad idea with OpenLDAP 2.4.36. You may want to read over the various sync issues that have been fixed since that release (Current release is 2.4.45). The only safe way for you to reload another server will be slapcat/slapadd.
Generally, I'd strongly advise upgrading to a current release and switching to back-mdb, eliminating BDB entirely.
--Quanah -- Quanah Gibson-Mount Product Architect Symas Corporation Packaged, certified, and supported LDAP solutions powered by OpenLDAP: <http://www.symas.com>