Directory entries deleted on one replica are maintained by Directory Server until no longer needed for replication. Such deleted entries are called tombstones, as they have objectclass: nsTombstone. In rare cases, you might need to remove tombstones manually over LDAP.
Tombstones visible only to Directory Manager. Furthermore, tombstones show up only in a search with filter (objectclass=nsTombstone). The following ldapsearch command returns tombstone entries under dc=example,dc=com.
$ ldapsearch -D "cn=Directory Manager" -b dc=example,dc=com "(objectclass=nsTombstone)"