I'm sorry to hear the situation really is as dire as you first said. Stressful indeed. I was about to suggest first trying to restore your course from a backup, but I see Jenny beat me to it. I agree with her that this doesn't sound like a CodeRunner-related problem.
My suggestion of saving questions to a different category doesn't work, sorry. That functionality is no longer present from within the question editor in Moodle 4.
It might be possible to get some sort of handle on what happened and to patch it using SQL commands, but hacking at the database is perilous and an absolute last resort. You must certainly back up the database before attempting any such operations. You'd want to look first at the question_categories and question_bank_entries tables.
My suggestion of saving questions to a different category doesn't work, sorry. That functionality is no longer present from within the question editor in Moodle 4.
It might be possible to get some sort of handle on what happened and to patch it using SQL commands, but hacking at the database is perilous and an absolute last resort. You must certainly back up the database before attempting any such operations. You'd want to look first at the question_categories and question_bank_entries tables.