I have upgraded openldap to latest stable version (2.3.38) and
used Berkeley DB version 4.5.20. The problem remains. I realize
my analisys wasn't correct since, as Howard Chu pointed out, the
CSN contains both a timestamp and a counter. So the entryCSN:s
are unique.
But, the problem remains and I have no idea why this happens.
I somehow still suspect that the problem still is in the initial
phase of the sync operation (refresh stage). It might be that,
some of the not-yet committed modifications don't make it into
the result set in the search operation. Later after another entry
is added, the "lost" entries are never to be synced over.