I've got a bizarre issue where one of my developers created an issuetype==Story and then added sub-tasks underneath that story. The story is visible on the Kanban board and has a status of "In Progress" but it's not visible in the Backlog view. The remaining sub-task that is still open is visible in the Backlog view but appears orphaned; the corresponding parent issue isn't visible. All other issues appear to be visible in the Backlog view.
In the past, I might have tried re-indexing but this option is no longer available.