Several people made changes to the templates (maybe core files, can’t tell) and there are few websites that are working directly on the bb tables. The problem is that upgrade would demand much more work than uploading new files and running upgrade.php. The owner of those websites wouldn’t be pleased with the downtime of some sort.
Well, one of way of dealing with this problem, that I think of, is to list all included files and backtrace all of the executed functions. Maybe that way I could find missing item.