We're been using 2.2, but am uprading to 2.5. The conversion was no problem, except for one of my classes (we have about 150 total classes, just my bad luck).
I did figure out how to delete them, simply go to my course home page, then click the "X" to delete it . I was looking at the page with all the Questionnaires and trying to delete it from there.
So I have deleted the questionnaires, but still no luck with backing up my course. I'll keep looking elsewhere for this problem...