We'll write an admin report (the 'Is your question bank ready for Moodle 1.9?' report) and check that in to the 1.8 and 1.7 stable branches. That report performs the same logic on your site as the upgrade would, and lists all the categories that would cause a problem if you upgraded now. This report can include lots of explanatory text, and have links to go and edit those categories manually, so people can easily tweak things by hand before upgrading if they want to. We can then point people to that report in the release notes.
The first steps in the db upgrade should proceed as follows :
1. Delete all random questions in the question bank that are not included in a quiz before upgrade. This should be safe. These questions have somehow become orphans and shouldn't be in the question bank anyway.
2. Then we work through all the category trees in the site, starting at the top, and every time we find a category with random questions picking from subcategories, we set all child categories to have the same published status as that one. We log the changes we make so they can be reviewed later and print a warning during the upgrade process.