Not quite sure if this is an issue, or a comment, or what....
When deleting a question from the questionnaire module, the question itself does not get deleted, but gets a flag in the database under the cell deleted, with y.'
Of course, when you import a questionnaire, or backup and restore a questionnaire, the deleted questions are also restored. (go figure)
The reason we found it, we have a course development site, and a live site. Once a course has been developed on the dev site, we back up the course and restore it on the live site. Because there was a deleted question in a template we use, and a file attached to that question in a repository has been removed, any time we use this we get an error on the restore.
I just did some testing on the ramifications, and then removed all the 'deleted' questions from our development site - I deleted just over 7000 questions, and left 4,500 questions remaining....
Cheers
Peter