Just to inform you, I'm following this thread.
Forgetting about .apnx files, all the other file types you list, I only see on my K3 for files downloaded directly from AMZ to K3, OR sent by browser amz.com to my K3.
Have never deleted any books on K3 from calibre, so I don't have any "sidecars".
But I'll keep track of this thread - I just might learn something new
Thanks for spotting this !
Brgds, Per