Our log level is stats and sync. The logs look like this, for the user being modified ----- nonpresent_callback: rid=005 present UUID 528929d6-acaa-1036-922a-a3f5c9285d9d, dn uid=xxx,ou=users,dc=ruc,dc=dk Entry uid=xxx,ou=users,dc=ruc,dc=dk CSN 20170406140323.504919Z#000000#002#000000 greater than snapshot 20170403102309.253881Z#000000#002#000000
It would appear you have serious issues with your installation, since the CSNs are off by 3 days. I would note that 2.4.40 is not stable for MMR as well. I would ensure you aren't suffering from clock skew across your servers, and upgrade to the current OpenLDAP release as well.
--Quanah -- Quanah Gibson-Mount Product Architect Symas Corporation Packaged, certified, and supported LDAP solutions powered by OpenLDAP: <http://www.symas.com>