Whether it is from top to bottom or bottom to top...
Authors moved some bulk of the articles from some Folder1 to some Folder2. However, couple of days after moving the files, they again re-appeared in Folder1 of Runtime application. It was surprising on how they came up. My theory is that since the files that were moved had not been submitted to staging (which means the files are still present in the staging at the old location) the staging had duplicate entries for the same files. During deployment the script might had updated the database to sync up the properties (file path) from Folder1. And when it found the same files in Folder2 it might had considered them as duplicate.