All services are not functional because most core files have zero size, so I've moved some of '~' files to normal ones and "temporarily" solved problem and started all services so users using server are ok with services. webmail, phpmyadmin, ispconfig do not work.
That was the right procedure to get the system services back running.
I dont know what exactly happened, according to the log it seems as if the directory of the process that was running the update changed while the update was installed so that the update could not open its template files and then wrote empty files instead. I guess there must be some kind of race condition or interference with other cronjobs. I will disable the autoupdate function in the Interface until we find the reason for this, the normal shell update seems not to be affected.
Do you have a backup of the files /usr/local/ispconfig/server/lib/config.inc.php and /usr/local/ispconfig/server/lib/mysql_clientdb.conf for all servers somewhere? The backup can be older as the content does not change.
If not, we can rebuild these files from the templates, but using a backup would be easier.