It's currently not possible to change the location of the log4j.properties file on windows. The value of LOG4J_CONFIG always gets replaced with the default value server\resources\log4j.properties. Thus, this file inside the server directory needs to be changed after every update.
See attached patch for a fix. Unfortunately, I couldn't figure out why LOG4J_CONFIG was set to empty. I tested manually that logging still works when running an example so I hope that this line is really just obsolete.