Big thanks for your reply, it seems to work now!
Just for completion:
I rebooted the remote machine to make sure no ressource is occupied and then
deleted all files in silent/database folder except shrubbot.cfg (which looked valid) and
every log files generated I found to make a clean start over.
Im not using any starting script (daemon, watchdog etc.) to run the server in background,
but rather I keep the process running in a window in a screen session so I can always attach to it.
Therefore I have to dissent not to use "/rcon quit",
because I can see the full shutdown sequence with writing and closing the databases.
After attaching to the session I can logically see that I'm back on command prompt.
No concurrent processes are fired. I guess the database got corrupted after just killing (ctrl+c) the process,
while it was trying to write stats on disk and had a problem to parse afterwards.
Maybe sending a SIGTERM signal would be more appropriate (haven't tried yet), but first mentioned possibility to quit does the job pretty well.
To handle this task easier not needing to rcon all the time I defined the easy custom command:
[command]
command = shutdown
exec = quit
desc = Shuts down the server
syntax = [name]
levels = 7
It's not a big deal to hit key up and launch ./startserver again!
However a linux console solution to get this quit triggered ingame would be really great! (no idea yet)
Greets!