Large amount of entity revision cleaning leads to connection abortion
It turned out what the real issue was. I didn't mention (thought it's not important) that this was actually a Drush command pointing to another multi site. 

The actions took "too long" on the other site and by the time it returned with success, the default Mysql connection was timed out and couldn't write to the database anymore. (even tho the corresponding Mysql timeout settings were way higher than the actual amount of time that was spent on the other site)

We solved with with 

$process = proc_open($command, [STDIN, STDOUT, STDERR], $pipes);
if (!is_resource($process)) {
  throw new \InvalidArgumentException("Could not execute `{$command}`.");
}
while (($status = proc_get_status($process)) &amp;&amp; ($status['running'])) {
  $this-&gt;entityStorage-&gt;getQuery()-&gt;count()-&gt;execute();
  sleep(5);
}
proc_close($process);