Hi @bwilhelm,
thanks for your reply, you were correct.
I tried to recreate the problem and failed at recreating it - it behaved as you said it should. 
The configuration windows replayed the last Python output and it did NOT overwrite my log files.
My best guess at what happened before would be that maybe I got confused by the replay of the output and also checked log files in a wrong folder by accident?
Anyhow, we can close the topic. Thanks for your time! Your reply helped me re-assess the (non-)issue. At the least, I now know that the Python Script Node works as I would have expected it to work. 