I did change the installation file and managed to stop and start kiwix-serve during USB connect. Since "/usr/local/Kobo/udev/usb" changed during recent updates, there are 2 installation files now, depending on the firmware version.
If the wrong version is installed, USB connection ist lost. To prevent accidental bricking of devices I wrote an extensive tutorial in German and English. Hope that someone will find it useful. Went back to the older version of kiwix-serve, since I couldn't find any flaws in it and it seems to be supporting more devices. Everything can be downloaded at:
http://bit.ly/2zlYaCL