In the GUI I could see, that the value of INDEX for "up-to-date" was "false".

this information simply indicates that not all index structures are updated yet. Whenever you activate UPDINDEX, your text and value will always be updated (i.e., "Text Index: " should always be followed by the flag "ON").

OK, I will have a look at this as soon as I can start my application again.

nothing happens. It looks like the script is waiting for some input -- the process does not stop.  The old BaseX server seems to be running somehow; I cannot start the server either.

maybe there's still a process running server-side? What output do you get when calling the SHOW SESSIONS command?

It says 0 sessions.  However, calling "basexserver" from the command line gives:

Server ist running or permission was denied

It has nothing to do with user rights, the "permission" part does not apply. 

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".

Any ideas?