Did you install snort? The snort package had a bug that caused the admin user to clash with the snort user. I don’t think this can make admin disappear, but it’s the only idea I have now.
Details here:
http://dev.nethserver.org/issues/3163
No, i haven’t install snort.
The server is used as file server and as webserver for an internal (only internal lan) data exchange application.
The issue seems to be (a big) ldap database corruption, as stephdl said. Probably it was caused by anything that go wrong during the backup that is the only thing that work during the night 
Now i disabled the backup process temporarily .