(maybe reconsider your headline - the topic is I think different) - this behaviour (lost flows, or also lost other elements) can happen if you move flows from one location in the category tree and do not paste them somewhere else, or if you delete the parent category via python or sql for example. Normally this can be easily fixed but you would need to use SQL for this. Like:
update tbl_categories set f_category = null where f_category not in (select id from tbl_categories)
(in the SQL window)
Make a backup of the database before. This moves all "lost" elements to their respective top category.