Ken and Sèverin,
Last night I finally got the backup running.
And in retrospect, it was quite easy to find out what the problem was. (isn't it always).
I used Severin's script in one command line as cron, However, that still didn't work. What happened was that on this Cpanel the max_execution_time=36000 was not accepted. It was being overridden somehow, which led to a timeout.
Moodle never gives you a hint about this time-out. Things just stop. What's even more weird is that even if I ran the backup script every hour, I only saw like 4 courses being backupped every couple of days.
Finally I got to increase the max_execution_time to 36000 and every course seems to be backed up.
The proces took about 9 hours to run. Then this mail came:
Summary
==================================================
Courses; 7200
OK; 5793
Skipped; 1395
Error; 0
Unfinished; 12
Warning; 0
Automated backup pending; 0
Some of your courses weren't saved!!
Just need to look at the 12 unfinished courses now... but this seems great.
Thanks Ken and Sèverin for your info and patience