FWIW, I can confirm that Qkn does, indeed, make its automatic backups in a Backup Folder in the Folder in which the QDF File resides.
So, if multiple QDF's exist in the same Folder then all of their auto-backups will go to the same Backup Folder. If, however, the multi-QDF's each lived in a Folder of its own then the backups will go to each separate Backup Folder.
For an nu-related reason I had a Qkn Copy File that I had made to a separate Folder for isolation.
After completing the the reason for the copy I then opened and closed that separate file over the course of the last several days.
Today, after reaching the auto-threshold, when I exited Qkn it created a Backup Folder in my separate Copy Folder and put it's auto-backup in that newly created Folder.
So have each Qkn File in a Folder of its own and have links (Desktop or elsewhere) to open each File.
Geo. Salisbury Long Valley, NJ