I don't know if you want to change your instructions a bit though?
rather than editing qmail-scanner-queue.py (it is .pl in the Perl version anyway), change /etc/qmail-scanner.ini then run qmail-scanner-reconfigure
I don't know if you are using something different (because of the python .py extension) but in the versions I use ( Perl .pl), every time you run qmail-scanner-reconfigure, it will overwrite the qmail-scanner-queue.pl with the settings from qmail-scanner.ini
Edit: Also you might want to change the bash script that copies the messages so that it checks if something new is in the new folder or not, otherwise you'll get a nessage from cron saying it can't copy anything
Or you could just add a >/dev/null 2>&1 jobbie to the end of the cron command.