When trying to call "basexserver stop", nothing happens, it seems to wait for something or process something. When I call basexserver stop, "java" appears for a moment in "top", but then it disappears and the command does not stop. Very frustrating. Calling "basexserver -S", shows the same behavior -- although you would expect the same message like the one for "basexserver".
Difficult to guess what’s going on here. My assumption is that there must be a process waiting for something, and as the "stop" command tries to gracefully shut shown the server, it won’t do anything.
Using Linux, you could check the list of open files and grep the result for any basex-related files (eg: lsof | grep -i basex). If there no database files are touched, it should be a safe bet to simply kill your server process. By the way, even if the process is killed, the server will try to flush and close open databases.
Hope this helps, Christian